@Copyright INRAE

Software application registered with the APP1,

IDDN.FR.001.170026.003.R.P.1999.000.30100

JavaStics V1.5.0 / STICS V10.0.0

User guide

Software maintainers

Dominique RIPOCHE-WACHTER

Patrice LECHARPENTIER

Contact : D. Ripoche-Wachter, P. Lecharpentier US1116 Agroclim INRA Centre de recherche INRA 228, route de l’aErodrome, CS 40509 Domaine St Paul, Site Agroparc 84914 Avignon cedex 9, France E-mail : ,

1 Preface

JavaStics V1.5.0 is an interface for managing simulations with the STICS V10.0.0 crop model on Windows, Linux and Mac OS platforms. This tool provides a user-friendly environment for managing input-output to and from the models and for their operational use.

This documentation is far from being exhaustive. It should be considered as a description summary of each menu, intended to guide the beginning user.

Please read this user license attentively before using the software.

USER LICENSE

Copyright © INRAE

All rights reserved

The version Nr 4 of STICS (JavaStics_reference_4.0 + src_ModuloStics_v1.0) was filed in 2011 with the APP,
under the deposit number IDDN.FR.001.170026.003.R.P.1999.000.30100

The version 9.0 of the STICS code was filed in 2020 with the APP,
under the deposit number IDDN.FR.001.360007.000.S.C.2021.000.10000

Software manager:

INRAE –STICS Project Team

https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team

INRAE is designated below as “the Copyright Holder”

The Terms and Conditions of Use of the software are defined below. Redistribution and use in source and binary forms, with or without modification, are permitted for NON-COMMERCIAL purposes provided that the following conditions are met:

  1. Permission to use, copy and modify this software and its documentation for NON-COMMERCIAL purposes is granted, without fee, provided that an acknowledgement to the Copyright Holders, appears in all copies and associated documentation or publications.

  2. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  3. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

  4. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The version V10.0.0 of the STICS sources code are on Cecill C ( see details 2.2)

The JavaStics sources are not supplied.

2 Introduction

The STICS model simulates, at a daily time-step, the soil-crop system behaviour of a single field context (1-D model), over one or several successive crop cycles. STICS can simulate annual and perennials crops as well as intercropping systems.

This notice will not present the formalisations of the STICS model, but only the way of using the software JavaStics and the model in a practical way.

The modelled system, the conceptual framework and the simulated processes are fully described in the 2 first chapters of the OpenStics book. If the user wants to know more in detail about the formalisms, we recommend him to refer to the new OpenStics book (mettre le lien).

2.1 Purpose

JavaSTICS is the software associated to STICS for facilitating its use. It is a friendly user interface which allows to understand and use the model features for various actions, such as i) creating or modifying “USMs” (unit of simulation) and parameters files needed for simulations, ii) managing the inputs data, iii) running the model in different ways, iv) visualising a selection of output variables (eventually gathered with observations data), and also v) optimising parameters using observed data.

JavaSTICS helps users to prepare and launch multi-simulations such as: long-term simulations, rotations, intercropping, etc. In addition, the STICS executable can be managed by using the JavaSTICS command line interface to facilitate complex experiment plans management involving many simulations to be run using various software languages (such as R language) and also platforms.

JavaSTICS and the model are freely downloadable from the STICS web site (http://www6.paca.inrae.fr/stics_eng), as well software documentation and other documents about formalisms description.

2.2 The source code licence

The Stics code source is developed by open source project and licensed under the term of version 1.0 of the CeCILL-C license (CECILL-C Free Software License Agreement, https://cecill.info/licences.en.html or https://spdx.org/licenses/CECILL-C.html#licenseText )

The sources are downloadable on the Stics forge:

https://w3.avignon.inra.fr/forge/projects/stics_main_projecv/files

2.3 Installation

The JavaStics interface and the STICS model are available on the STICS Web site through a registration procedure accessible at https://www6.paca.inrae.fr/stics_eng/Download. The downloaded .zip file should be unzipped to an independent JavaStics directory. The model executables for Windows and linux are all included in this zip.

If you already have an earlier version of JavaStics, unzip it to a new directory rather than to the existing one. Be carefull not to install this JavaStics folder on the desktop and avoid folder names with blanks in the directory path.

On linux and Mac OS X platforms Java JRE or SDK must be installed to run the JavaStics interface

TODO: introduce prerequisites ! Specific version : java 11 !!!!!!!!!, update above info

Java Oracle: https://docs.oracle.com/javase/8/docs/technotes/guides/install/linux_jdk.html

OpenJDK: http://openjdk.java.net/install

On Mac OS X, Fortran libraries must be installed for running the Stics model. To do so, command line tools installation is needed.

Simply check if they are already installed by typing gfortran in a terminal. If they aren’t installed, a window will appear to proceed to their installation after clicking on Install and accepting the licence.

We can check if command line tools are installed by typing xcode-select –p and enter, /Library/Developer/CommandLineTools will be displayed in the terminal.

Fortran installation can be checked by typing gfortran in the terminal. An error message will be displayed:

gfortran: fatal error: no iput files

compilation terminated.

2.4 Organisation of files and directories

In the JavaStics directory, you will find a number of files and subdirectories:

We will point out the most important ones:

  • JavaStics.exe: executable file for launching the JavaStics graphical interface

  • JavaSticsCmd.exe: executable file for launching the JavaStics command line tool (using options)

  • the config directory: contains general settings files

  • the default directory: contains the configuration for creating a new directory

  • the example directory: contains examples that you can use to test the interface and the model

  • the bin directory: contains the executables, the resources and the libraries needed by the interface

    • Windows executable: stics_modulo.exe (model), ajustJavaStics.exe

    • Linux executable: stics_modulo (model), ajustJavaStics

  • the logs directory: contains the log files (of user interventions and application)

  • the plant directory: includes the settings files for each crop supported by the STICS model.

  • the doc directory: contains the JavaStics documentation, a changes file and some articles.

User directories are workspaces that may be created either by adding a new working directory or by launching a reformatting process (for STICS older version files).

Directories configuration

Figure 2.1: Directories configuration

To perform a simulation, JavaStics is using different XML files located in two fixed directories: config, plant and user defined workspace(s) directorie(s). JavaStics allows the user to modify these files and creates them as shown on the figure below. These input files are created in the user workspace(s).

Files workflow

Figure 2.2: Files workflow

The Stics model itself can be used directly without the JavaStics interface, but you must use the text files created by JavaStics as input files (.txt, .sti, .sol and .usm) and not the XML files.

TODO: add link to the R packages section for text files generation apart from JavaStics GUI or command line.

You can generate these txt files from XML ones as explained in the “Using JavaStics command line tool” section.

2.5 Launching JavaStics

TO BE FIXED FOR LINUX ! Be aware that java must correspond to a java version 11 executable known by the system (i.e. declared in the PATH environment variable) If not, an alias can be used instead (containing a full java 11 path), or explicitely the full path to a java 11 executable

2.5.1 The JavaStics GUI

For the Windows systems double-click on JavaStics.exe from the file manager. The main JavaStics window appears.

For the linux or Mac OS X systems, execute the following command in the JavaStics root directory from a terminal:

java -jar JavaStics.exe

You may use also an absolute path too:

java -jar /path/to/JavaStics/directory/JavasStics.exe

2.5.2 The JavaStics command line

The old JavaSticsCmd.exe executable does not exist anymore, the unique executable is using options for executing commands for Stics using from a terminal for Unix like OSes or a command prompt window (CMD) under Windows.

Any call to the command line must be done from the JavaStics root folder in a terminal or a command prompt window.

In order to display the command manual/help, take care of the OSes specificities mentionned above. java -jar must be added before JavaSticsCmd.exe in the command call.

  • for Windows
    JavaSticsCmd.exe -help
    or 
    JavaSticsCmd.exe -h
    
  • For linux/Mac
    java -jar JavaSticsCmd.exe -help
    or
    java -jar JavaSticsCmd.exe -h
    

Here after are described the command line options and the associated needed information displayed in the command line help. The Windows command syntax is used in examples. The example workspace included in the JavaStics folder is used in commands examples and can directly be executed. Relative or absolute paths may be used for specifying the workspace to be used.

Options Action Examples
-v, --verbose Get command line help JavaStics.exe -v
JavaStics.exe -v --run example maize
--run [WORKSPACE] Run all USM from a workspace JavaStics.exe --run example
--run [WORKSPACE] [USM1] [USM2] … Run specified USM from a workspace JavaStics.exe --run example soybean
JavaStics.exe –run example wheat maize
--run [WORKSPACE] [USM1] [USM2] … Run specified USM successively from a workspace JavaStics.exe --run-successive example demo_Wheat1 demo_BareSoil2 demo_maize3
--generate-txt [WORKSPACE] [USM] Generate Stics text input files for a specified USM a workspace JavaStics.exe --generate-txt example wheat

Sample batch files (example_batch.bat, for Windows or example_batch.sh, for linux) are available in the JavaStics root directory.

3 General Menu

3.1 Main entries

The main menu items of the JavaStics interface are organised as follows:

  • File: select or create a simulation directory. The simulation directory contains the parameter files that can be edited by the user and also the STICS output files too.

  • Model inputs: view and edit STICS input files

  • Running model: launch simulations

  • Model outputs: select outputs (before simulation) and view the model outputs when the simulation is done

  • Observations: process observed data

  • Tools: tools for selecting or adding others versions of STICS than the standard version

  • Help: display the application version

The JavaStics Window

Figure 3.1: The JavaStics Window

3.2 File

To perform simulations with the STICS model, you must first define simulation units (USMs) which correspond to a climate, a soil and a crop management. The parameter files describing the USMs are stored in a working directory called workspace.

The first step before running a simulation is to define the workspace where the input files are stored. You can either create a new workspace using File/New workspace or select an existing one File/Open workspace.

General menu

Figure 3.2: General menu

3.2.1 New workspace

This menu lets you create a new working directory. This directory will contain only a USM example and a set of files corresponding to this USM.

The workspace directory can be located anywhere on your disk.

It can be an existing directory or you can create it by clicking on the “Create directory” Windows icon.

Choose the directory, and then click Open. JavaStics considers it as an empty directory as far as the application is concerned. Therefore, the USM example files will be created.

3.2.2 Open workspace

This menu can also be invoked via the icon

It lets you select an existing workspace directory. This directory will be the current user directory as long as it is not changed.

The workspace path is saved and reloaded as starting workspace when the interface is launched again.

Choose the workspace directory, and then click Open.

The name and path of the selected workspace appears in the main window title bar, so the user can verify this is the workspace he wants to use.

3.2.3 Historic display

This menu lets you view the log of your actions in the interface. This log file user_log.txt contains an history of all actions done using the interface and is stored in the logs directory. Until this file is deleted, it keeps information about all the JavaStics sessions.

3.2.4 Switch theme

This menu lets you to switch between two themes for windows: a light mode or a night one as showed here after:

or

3.3 Model Inputs

3.3.1 Global parameters

To view or edit the global parameters, choose Model inputs/Global parameters/General parameters for accessing to the param_gen.xml or the param_newform.xml files.

Global parameters

Figure 3.3: Global parameters

3.3.1.1 Parameters contained in the param_gen.xml file

Table 3.1: Table of parameters contained in the param_gen.xml file
Name Definition Unit
ahres parameter of organic residues humification: hres=1-ahres*CsurNres/(bhres+CsurNres) \(\mathrm{ND}\)
akres parameter of organic residues decomposition: kres=akres+bkres/CsurNres \(\mathrm{day^{-1}}\)
albedomulchresidus albedo of plant mulch \(\mathrm{ND}\)
alphapH maximal soil pH variation per unit of inorganic N added with slurry \(\mathrm{kg^{-1}\ ha}\)
awb parameter determining C/N ratio of biomass during organic residues decomposition: CsurNbio=awb+bwb/CsurNres \(\mathrm{g\ g^{-1}}\)
beta parameter of increase of maximal transpiration when a water stress occurs \(\mathrm{ND}\)
bformnappe coefficient for the water table shape (artificially drained soil) \(\mathrm{ND}\)
bhres parameter of organic residues humification: hres=1-ahres*CsurNres/(bhres+CsurNres) \(\mathrm{g\ g^{-1}}\)
bkres potential rate of decomposition of organic residues: kres=akres+bkres/CsurNres \(\mathrm{g\ g^{-1}}\)
bwb parameter determining C/N ratio of biomass during organic residues decomposition: CsurNbio=awb+bwb/CsurNres \(\mathrm{g\ g^{-1}}\)
cmax_pdenit Soil organic carbon concentration above which denitrification potential is constant and maximum \(\mathrm{g\ kg^{-1}}\)
cmin_pdenit Soil organic carbon concentration below which denitrification potential is constant and minimum \(\mathrm{g\ kg^{-1}}\)
CNresmax maximum value of C/N ratio of organic residue \(\mathrm{g\ g^{-1}}\)
CNresmin minimum value of C/N ratio of organic residue \(\mathrm{g\ g^{-1}}\)
code_hourly_wfps_denit option to activate hourly WFPS calculation for denitrification: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_hourly_wfps_nit option to activate hourly WFPS calculation for nitrification: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_pdenit option to define the denitrification potential: 1 = read in soil parameter, 2 = calculated from soil organic carbon concentration \(\mathrm{code,\ 1\ to\ 2}\)
code_ratiodenit option to define the N2O/(N2+N2O) ratio of denitrification: 1 = constant, 2 = variable \(\mathrm{code,\ 1\ to\ 2}\)
code_rationit option to define the N2O/(N2+N2O) ratio of nitrification: 1 = constant, 2 = variable \(\mathrm{code,\ 1\ to\ 2}\)
code_tnit option to define the temperature function for nitrification: 1 = piecewise linear, 2 = gaussian \(\mathrm{code,\ 1\ to\ 2}\)
code_vnit option to define the nitrification rate dependence on NH4: 1 = first order, 2 = Michaelis-Menten \(\mathrm{code,\ 1\ to\ 2}\)
codeactimulch option to activate the mulch effect at soil surface: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codefrmur option to define the maturity status of the fruits in the variable CHARGEFRUIT: 1 = including ripe fruits (last box N), 2 = excluding ripe fruits (first N-1 boxes) \(\mathrm{code,\ 1\ to\ 2}\)
codefxn option to define the effect of soil nitrate on N fixation: 1 = no effect, 2 = effect of nitrate amount, 3 = effect of nitrate concentration \(\mathrm{code,\ 1\ to\ 3}\)
codeh2oact option to activate water stress effect on crop growth: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeinitprec option to activate reset of initial conditions in case of chained simulations: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeinnact option to activate N stress effect on root length growth: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codemicheur option to calculate hourly microclimatic outputs (output file humidite.sti): 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeminopt option to simulate a bare soil with a constant water content: 1 = yes, 2 = no \(\mathrm{code,\ 0\ to\ 1}\)
codemsfinal option to define if the biomass and yield are conserved after harvest: 1 = yes, 2 = no (values set at 0) \(\mathrm{code,\ 1\ to\ 2}\)
codeoutscient option to write outputs files with scientific format: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeprofmes option of soil depth for calculating water and N stocks (1 = profmes, 2 = soil depth) \(\mathrm{code,\ 1\ to\ 2}\)
codesensibilite option to activate the sensitivity analysis version of the model: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeseprapport option to select the column separator in the rapport.sti output file: 1 = space separator, 2 = separator indicated in the file rapport.sti \(\mathrm{code,\ 1\ to\ 2}\)
codesnow option to activate the snow module: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codesymbiose option to calculate symbiotic N fixation: 1 = based on critical dilution curve, 2 = specific calculation of N fixation \(\mathrm{code,\ 1\ to\ 2}\)
codetycailloux code for pebble type \(\mathrm{code,\ 1\ to\ 10}\)
codetypeng code for fertiliser type \(\mathrm{code,\ 1\ to\ 8}\)
codetypres code for organic residue \(\mathrm{code,\ 1\ to\ 10}\)
codhnappe option to calculate the watertable level : 1 = mean height, 2 = height at the distance distdrain \(\mathrm{code,\ 1\ to\ 2}\)
coefb parameter defining the radiation saturation effect on biomass conversion efficiency \(\mathrm{g\ MJ^{-1}}\)
CroCo fraction of organic residue which is decomposable \(\mathrm{ND}\)
cwb minimum ratio C/N of microbial biomass decomposing organic residues \(\mathrm{g\ g^{-1}}\)
dacohes bulk density of soil below which root growth is reduced due to a lack of soil cohesion \(\mathrm{g\ cm^{-3}}\)
daseuilbas bulk density of soil above which root growth is maximal \(\mathrm{g\ cm^{-3}}\)
daseuilhaut bulk density of soil above which root growth becomes impossible \(\mathrm{g\ cm^{-3}}\)
deneng maximal fraction of the mineral fertilizer that can be denitrified (used if codedenit is not activated) \(\mathrm{ND}\)
difN diffusion coefficient of nitrate in soil at field capacity \(\mathrm{cm^{2}\ day^{-1}}\)
diftherm soil thermal diffusivity \(\mathrm{cm^{2}\ s^{-1}}\)
distdrain distance between mole drains \(\mathrm{cm}\)
dpHvolmax maximal pH increase following the application of slurry \(\mathrm{ND}\)
engamm fraction of ammonium in the N fertilizer \(\mathrm{ND}\)
fhminsat relative soil mineralisation rate at water saturation \(\mathrm{ND}\)
flagecriture option for writing the output files (1 = mod_history.sti, 2=daily outputs,4= report outputs, 8=balance outputs,16 = profile outputs, 32= debug outputs, 64 = screen outputs) sum them to have several types of outputs \(\mathrm{ND}\)
fNCbiomin minimal value for the ratio N/C of the microbial biomass when N limits decomposition \(\mathrm{g\ g^{-1}}\)
fnx maximum fraction of NH4 nitrified each day (first order model) \(\mathrm{ND}\)
fredkN reduction factor of decomposition rate of organic residues when mineral N is limiting \(\mathrm{ND}\)
fredlN reduction factor of decomposition rate of microbial biomass when mineral N is limiting \(\mathrm{ND}\)
fredNsup additional reduction factor of residues decomposition rate when mineral N is highly limiting \(\mathrm{ND}\)
ftemh parameter (1/2) of the temperature function on humus decomposition rate \(\mathrm{K^{-1}}\)
ftemha parameter (2/2) of the temperature function on humus decomposition rate \(\mathrm{ND}\)
ftemr parameter (1/2) of the temperature function on decomposition rate of organic residues \(\mathrm{K^{-1}}\)
ftemra parameter (2/2) of the temperature function on decomposition rate of organic residues \(\mathrm{ND}\)
GMIN1 parameter (1/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{day^{-1}}\)
GMIN2 parameter (2/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{-1\%}\)
GMIN3 parameter (3/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{-1\%}\)
GMIN4 parameter (4/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{pH^{-1}}\)
GMIN5 parameter (5/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{pH}\)
GMIN6 parameter (6/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{g\ g^{-1}}\)
GMIN7 parameter (7/7) of the new mineralization function (Clivot et al, 2017) \(\mathrm{g\ g^{-1}}\)
hcccx gravimetric water content at field capacity of each type of pebble (dry soil) \(\mathrm{\%}\)
hminm relative water content (fraction of field capacity) below which mineralisation rate is nil \(\mathrm{ND}\)
hminn relative water content (fraction of field capacity) below which nitrification rate is nil \(\mathrm{ND}\)
hoptm relative water content (fraction of field capacity) above which mineralisation rate is maximum \(\mathrm{ND}\)
hoptn relative water content (fraction of field capacity) above which nitrification rate is maximum \(\mathrm{ND}\)
iniprofil option of smoothing out the initial mineral N and water profiles (spline function): 0 = no, 1 = yes \(\mathrm{ND}\)
irrlev amount of irrigation applied automatically on the sowing day to allow germination when the model calculates irrigation \(\mathrm{mm}\)
Kamm affinity constant for NH4 in nitrification (if Michaelis_Menten formalism is used) \(\mathrm{mg\ L^{-1}}\)
kbio potential decay rate of microbial biomass decomposing organic residues \(\mathrm{day^{-1}}\)
kcouvmlch extinction coefficient connecting the soil cover to the amount of plant mulch \(\mathrm{ND}\)
Kd Affinity constant for nitrate in denitrification \(\mathrm{mg\ L^{-1}}\)
kdesat rate constant of de-saturation \(\mathrm{day^{-1}}\)
lvopt root length density (RLD) above which water and N uptake are maximum and independent of RLD \(\mathrm{cm\ cm^{-3}}\)
masvolcx bulk density of each type of pebble \(\mathrm{g\ cm^{-3}}\)
max_pdenit maximal value of the denitrification potential (if code_pdenit = 2) \(\mathrm{kg\ ha^{-1}\ cm^{-1}\ day^{-1}}\)
min_pdenit minimal value of the denitrification potential (if code_pdenit = 2) \(\mathrm{kg\ ha^{-1}\ cm^{-1}\ day^{-1}}\)
mouillabilmulch maximum wettability of crop mulch \(\mathrm{mm\ t^{-1}\ ha}\)
nh4_min minimum (fixed ?) NH4 concentration found in soil \(\mathrm{mg\ kg^{-1}}\)
orgeng maximal amount of fertilizer N that can be immobilized in the soil (fraction for type 8) \(\mathrm{kg\ ha^{-1}}\)
parsurrg fraction of photosynthetically active radiation in global radiation (PAR/RG) \(\mathrm{ND}\)
pHmaxden pH beyond which the N2O molar fraction in the denitrification process is minimum (<= ratiodenit) \(\mathrm{pH}\)
pHmaxnit soil pH above which nitrification rate is maximum \(\mathrm{pH}\)
pHmaxvol soil pH above which NH3 volatilisation derived from fertiliser is maximum \(\mathrm{pH}\)
pHminden pH below which the N2O molar fraction in the denitrification process is maximum (100% ) \(\mathrm{pH}\)
pHminnit soil pH below which nitrification is nil \(\mathrm{pH}\)
pHminvol soil pH below which NH3 volatilisation derived from fertiliser is nil \(\mathrm{pH}\)
pHvols parameter used to calculate the variation of soil pH after the addition of slurry \(\mathrm{pH}\)
plNmin minimal amount of rain required to start an automatic N fertilisation \(\mathrm{mm\ day^{-1}}\)
pminruis minimal amount of rain required to produce runoff \(\mathrm{mm\ day^{-1}}\)
primingmax maximum priming ratio (relative to SOM decomposition rate) \(\mathrm{ND}\)
proflabour minimal soil depth for ploughing (if soil compaction is activated) \(\mathrm{cm}\)
proftravmin minimal soil depth for chisel tillage (if soil compaction is activated) \(\mathrm{cm}\)
prophumtassrec soil moisture content (fraction of field capacity) above which compaction may occur and delay harvest \(\mathrm{ND}\)
prophumtasssem soil moisture content (fraction of field capacity) above which compaction may occur and delay sowing \(\mathrm{ND}\)
proprac ratio of root mass to aerial mass at harvest \(\mathrm{ND}\)
psihucc soil water potential corresponding to field capacity \(\mathrm{MPa}\)
psihumin soil water potential corresponding to wilting point \(\mathrm{MPa}\)
qmulchdec maximal amount of decomposable mulch \(\mathrm{t\ ha^{-1}}\)
qmulchruis0 amount of mulch above which runoff is suppressed \(\mathrm{t\ ha^{-1}}\)
QNpltminINN minimal amount of N in the plant required to compute INN \(\mathrm{kg\ ha^{-1}}\)
ratiodenit fraction of N2O emitted per unit of N denitrified \(\mathrm{ND}\)
rationit fraction of N2O emitted per unit of N nitrified \(\mathrm{ND}\)
rdrain radius of the mole drains \(\mathrm{cm}\)
scale_tdenitopt parameter related to the range of optimum temperature for denitrification \(\mathrm{ND}\)
scale_tnitopt parameter related to the range of optimum temperature for nitrification \(\mathrm{ND}\)
separateurrapport column separator in rapport.sti file \(\mathrm{ND}\)
tdenitopt_gauss optimum temperature for denitrification \(\mathrm{^{\circ}C}\)
tmin_mineralisation minimal temperature for decomposition of humified organic matter \(\mathrm{^{\circ}C}\)
tnitmax maximal temperature above which nitrification stops \(\mathrm{^{\circ}C}\)
tnitmin minimal temperature below which nitrification stops \(\mathrm{^{\circ}C}\)
tnitopt optimal temperature (1/2) for nitrification \(\mathrm{^{\circ}C}\)
tnitopt_gauss optimal temperature (1/2) for nitrification \(\mathrm{^{\circ}C}\)
tnitopt2 optimal temperature (2/2) for nitrification \(\mathrm{^{\circ}C}\)
trefh reference temperature for decomposition of humified organic matter \(\mathrm{^{\circ}C}\)
trefr reference temperature for decomposition of organic residues \(\mathrm{^{\circ}C}\)
Vabs2 N uptake rate at which fertilizer loss is divided by 2 \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
vnitmax maximum nitrification rate (if Michaelis-Menten formalism is used) \(\mathrm{mg\ kg^{-1}\ day^{-1}}\)
voleng maximal fraction of mineral fertilizer that can be volatilized \(\mathrm{ND}\)
wfpsc WFPS (Water filled porosity space) threshold above which denitrification occurs \(\mathrm{ND}\)
Wh N/C ratio of soil humus \(\mathrm{g\ g^{-1}}\)
Xorgmax maximal amount of N immobilised in soil derived from the mineral fertilizer \(\mathrm{kg\ ha^{-1}}\)
y0msrac minimal amount of root mass at harvest (when aerial biomass is nil) \(\mathrm{t\ ha^{-1}}\)
yres Carbon assimilation yield by the microbial biomass during crop residues decomposition \(\mathrm{ND}\)

3.3.1.2 Parameters contained in the param_newform.xml file

Table 3.2: Table of parameters contained in the param_newform.xml file
Name Definition Unit
codecalferti option to activate the automatic calculation of fertilisation rate: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_CsurNsol_dynamic option to activate the dynamic calculation of CsurNsol: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeNmindec option to activate the limitation of residues decomposition due lack of mineral N: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codepluiepoquet option to replace rainfall by irrigation at poquet depth in the case of poquet sowing: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
coderes_pature residue type used to simulate bovine feces: 1-10 \(\mathrm{code,\ 1\ to\ 10}\)
codeSWDRH optin to calculate the duration of surface wetness: 1=yes , 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codetesthumN option to define automatic N fertilisation calculation: 1 = based on rainfall, 2 = based on soil water content \(\mathrm{code,\ 1\ to\ 2}\)
codetrosee option to calculate hourly dew temperature : 1 = linear interpolation, 2 = sinusoidal interpolation (Debele Bekele et al, 2007) \(\mathrm{code,\ 1\ to\ 2}\)
coef_calcul_doseN crop N concentration below which there is no N return to the soil through animal urine \(\mathrm{g\ kg^{-1}}\)
coef_calcul_qres crop N concentration used to calculate animal feces from animal grass dry matter intake \(\mathrm{g\ kg^{-1}}\)
Crespc_pature C content in animal feces (FW) \(\mathrm{\%}\)
dosimxN maximum amount of fertiliser N applied daily (mode automatic fertilisation) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
eaures_pature water content of animal feces deposited on soil during grazing (FW) \(\mathrm{\%}\)
engrais_pature fertilizer type used to mimic urine excretion (1=ammonium nitrate, 2=UAN solution, 3=urea, 4=anhydrous ammonia, 5=ammonium sulfate, 6=ammonium phosphate, 7=calcium nitrate, 8= fixed efficiency fertiliser) \(\mathrm{ND}\)
fNmindecmin minimal fraction of mineral N available for residues decomposition (if codeNmindec is activated) \(\mathrm{ND}\)
humirac A revoir: 1 = la fonction F_humirac atteint un plateau (ancien code) / 2 = la fonction n atteint pas de plateau (identique a la phase germination-levee) \(\mathrm{ND}\)
nbjoursrrversirrig number of days during which rainfall is replaced by irrigation in the soil after a sowing poquet \(\mathrm{days}\)
Nminres_pature proportion of N mineral content in animal feces (FW) \(\mathrm{\%}\)
option_pature option to activate grazing in pastures: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
pertes_restit_ext fraction of animal feces and urine not returned in grazed paddocks (e.g. in resting area, milking parlour, housing and paths/roads) \(\mathrm{ND}\)
rapNmindec slope of the linear relationship between the fraction of mineral N available for residue decomposition and the amount of C in decomposing residues \(\mathrm{g\ g^{-1}}\)
ratiolN nitrogen stress index below which fertilisation is started in automatic mode (0 in manual mode) \(\mathrm{ND}\)

3.3.1.3 Parameters contained in the plant files

Table 3.3: Table of parameters contained in the plant.xml file
Name Definition Unit
abscission fraction of senescent leaves falling to the soil \(\mathrm{ND}\)
adens Interplant competition parameter \(\mathrm{ND}\)
adfol parameter determining the leaf density evolution within the chosen shape \(\mathrm{m^{-1}}\)
adil parameter of the critical dilution curve [Nplante]=adil MS^(-bdil) \(\mathrm{\%}\)
adilmax parameter of the maximum dilution curve [Nplante]=adilmax MS^(-bdilmax) \(\mathrm{\%}\)
afpf parameter of the logistic function defining sink strength of fruits (indeterminate growth) : relative fruit age at which growth is maximal \(\mathrm{ND}\)
afruitpot maximal number of set fruits per inflorescence and per degree day (indeterminate growth) \(\mathrm{fruits\ inflorescence^{-1}\ degree\ days^{-1}}\)
allocfrmax maximal daily allocation to fruits \(\mathrm{ND}\)
alloperirac allocation rate of the seed reserves (perisperm) to the rootlet growth \(\mathrm{ND}\)
alphaCO2 coefficient accounting for the modification of radiation use efficiency in case of atmospheric CO2 increase \(\mathrm{ND}\)
alphaphot parameter of photoperiodic effect on leaf lifespan \(\mathrm{ND}\)
ampfroid semi thermal amplitude for vernalising effect \(\mathrm{^{\circ}C}\)
bdens minimal plant density above which interplant competition starts \(\mathrm{m^{-2}}\)
bdil parameter of the critical dilution curve [Nplante]=adil MS^(-bdil) \(\mathrm{ND}\)
bdilmax parameter of the maximum dilution curve [Nplante]=adilmax MS^(-bdilmax) \(\mathrm{ND}\)
belong parameter of the curve of coleoptile elongation \(\mathrm{degree\ days^{-1}}\)
bfpf parameter of the logistic curve defining sink strength of fruits (indeterminate growth): maximum growth rate relative to maximum fruit weight \(\mathrm{ND}\)
celong parameter of the plantlet elongation curve \(\mathrm{ND}\)
cfpf parameter of the first potential growth phase of fruit, corresponding to an exponential type function describing the cell division phase \(\mathrm{ND}\)
cgrain slope of the relationship between grain number and growth rate \(\mathrm{t^{-1}\ m^{2}\ d}\)
cgrainv0 fraction of the maximal number of grains when growth rate is zero \(\mathrm{ND}\)
codazofruit option to activate the direct effect of N plant status on the fruit/grain number: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codazorac option to activate the effect of N stress on root partitioning within the soil profile: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codcalinflo option to calculate the inflorescences number: 1 = read in param.par, 2 = calculated at the amf stage \(\mathrm{code,\ 1\ to\ 2}\)
code_acti_reserve option to activate the simulation of Nitrogen and Carbon reserves: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_diff_root option to activate the simulation of 2 root classes: 1 =yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_WangEngel option to activate the effect of temperature on development units for emergence according to Wang et Engel (1998): 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_stress_root option to activate the preferential allocation of biomass to roots in case of water or N stress: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codebeso option to calculate water requirements: 1 = k.ETP approach, 2= resistive method \(\mathrm{code,\ 1\ to\ 2}\)
codebfroid option to calculate chilling requirements: 1 = no need, 2 = vernalising days, 3 = development stage \(\mathrm{code,\ 1\ to\ 3}\)
codedormance option to calculate dormancy and chilling requirements: 1 = forcing, 2 = Richardson, 3 = Bidabe \(\mathrm{code,\ 1\ to\ 3}\)
codedisrac option to define root profile in soil: 1 = standard root distribution, 2 = root emission proportional to root biomass \(\mathrm{code,\ 1\ to\ 2}\)
codedyntalle option to activate the module simulating tillers dynamics: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codefixpot option to calculate the maximal symbiotic fixation: 1 = fixed value read in the plant file, 2 = depends on growth rate \(\mathrm{code,\ 1\ to\ 2}\)
codegdh option to define the time step used for calculating development units: 1 = hourly, 2 = daily \(\mathrm{code,\ 1\ to\ 2}\)
codegdhdeb option to define the time step used for calculating bud break date: 1 = daily, 2 = hourly growing degrees \(\mathrm{code,\ 1\ to\ 2}\)
codegermin option to simulate germination: 1 = germination phase, 2 = immediate germination \(\mathrm{code,\ 1\ to\ 2}\)
codehypo option to simulate plant emergency: 1 = phase of hypocotyl growth (sown crops), 2 = plantation of plantlets \(\mathrm{code,\ 1\ to\ 2}\)
codeindetermin option to simulate the type of leaf growth and fruit growth: 1 = determinate, 2 = undeterminate \(\mathrm{code,\ 1\ to\ 2}\)
codeINN option to compute NNI: 1 = cumulative NNI, 2 = instantaneous NNI \(\mathrm{code,\ 1\ to\ 2}\)
codeintercept option to simulate rainfall interception by leaves: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeir option to calculate the ratio grain weight/total biomass: 1 = proportional to time, 2 = proportional to thermal time \(\mathrm{code,\ 1\ to\ 2}\)
codelaitr option to calculate the intercepted radiation according to: 1 = LAI, 2 = soil cover \(\mathrm{code,\ 1\ to\ 2}\)
codelegume option to define if the crop is a legume fixing N: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codemonocot option to define the type of plant: 1 = monocot, 2 =dicot \(\mathrm{code,\ 1\ to\ 2}\)
codemontaison option to stop the reserve limitation after stem elongation in grassland: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codemortalracine option to calculate the mass of dead roots after a cut: 1 = based on masec, 2 = based on masectot \(\mathrm{code,\ 1\ to\ 2}\)
codeperenne option to define the crop perenniality: 1 = annual crop, 2 = perennial crop \(\mathrm{code,\ 1\ to\ 2}\)
codephot option to define plant photoperiodism: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codephot_part simulation of the effect of decreasing photoperiod on biomass allocation : 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeplante option to define the coding name of the plant (3 characters) \(\mathrm{ND}\)
codeplisoleN option to define N requirements at the beginning of the cycle: 1 = dense plant population, 2 = isolated plants \(\mathrm{code,\ 1\ to\ 2}\)
coderacine option to define the calculation of root growth and extension: 1 = standard profile, 2 = root length density \(\mathrm{code,\ 1\ to\ 2}\)
coderetflo option to activate the effect of water stress on development before the stage DRP (filling of harvested organs): 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
code_rootdeposition code to simulate N demand and allocation to roots and their turn-over during crop growth cycle: 1 = daily deposition, 2 = deposition only at harvest \(\mathrm{code,\ 1\ to\ 2}\)
codestrphot option to activate the photoperiodic stress on lifespan (1 = yes, 2 = no) \(\mathrm{code,\ 1\ to\ 2}\)
codetemp option to calculate thermal time for plant growth: 1 = based on air temperature, 2 = based on crop temperature \(\mathrm{code,\ 1\ to\ 2}\)
codetemprac option to calculate thermal time for root growth: 1 = crop temperature, 2 = soil temperature \(\mathrm{code,\ 1\ to\ 2}\)
codetranspitalle option to choose the ratio used to calculate tiller mortality: 1 = et/etm, 2 = epc2/eopC \(\mathrm{code,\ 1\ to\ 2}\)
codetransrad option to calculate radiation interception: 1 = Beer law, 2 = radiative transfer \(\mathrm{code,\ 1\ to\ 2}\)
codetremp option to activate heat effect on grain filling: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codevar code for cultivar name \(\mathrm{ND}\)
codgelflo option to activate the frost effect at anthesis: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codgeljuv option to activate the frost effect on LAI at the juvenile stage: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codgellev option to activate the frost effect on plantlet growth: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codgelveg option to activate the frost effect on LAI at adult stage: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codlainet option to calculate the LAI: 1 = net LAI, 2 = difference between gross LAI and senescent LAI \(\mathrm{code,\ 1\ to\ 2}\)
codtrophrac option to activate a trophic effect on root length growth: 1 = permanent link, 2 = link by thresholds, 3 = no effect \(\mathrm{code,\ 1\ to\ 3}\)
coefamflax multiplier coefficient applied to the thermal time requirement between stages AMF and LAX \(\mathrm{ND}\)
coefdrpmat multiplier coefficient applied to the thermal time requirement between stages DRP and MAT \(\mathrm{ND}\)
coefflodrp multiplier coefficient applied to the thermal time requirement between stages FLO and DRP \(\mathrm{ND}\)
coeflaxsen multiplier coefficient applied to the thermal time requirement between stages LAX and SEN \(\mathrm{ND}\)
coeflevamf multiplier coefficient applied to the thermal time requirement between stages LEV and AMF \(\mathrm{ND}\)
coeflevdrp multiplier coefficient applied to the thermal time requirement between stages LEV and DRP \(\mathrm{ND}\)
coefmshaut ratio of crop biomass to useful cutting height of crops \(\mathrm{t\ ha^{-1}\ m^{-1}}\)
coefracoupe proportion of roots dying after a cut of a forage crop \(\mathrm{ND}\)
coefsenlan multiplier coefficient applied to the thermal time requirement between stages SEN and LAN \(\mathrm{ND}\)
concNnodseuil maximal concentration of mineral N in soil for nodule onset \(\mathrm{kg\ ha^{-1}\ mm^{-1}}\)
concNrac0 nitrate-N concentration (if codefxN=3) or nitrate-N amount (if codefxN=2) above which N fixation is totally inhibited \(\mathrm{kg\ ha^{-1}\ mm^{-1}\ or\ kg\ ha^{-1}\ cm^{-1}}\)
concNrac100 nitrate-N concentration (if codefxN=3) or nitrate-N amount (if codefxN=2) below which N fixation is maximum \(\mathrm{kg\ ha^{-1}\ mm^{-1}\ or\ kg\ ha^{-1}\ cm^{-2}}\)
contrdamax maximal reduction factor applied to root growth rate due to soil strengthness (high bulk density) \(\mathrm{ND}\)
croirac elongation rate of the root apex \(\mathrm{cm\ degree\ days^{-1}}\)
debsenrac thermal time units defining the beginning of root senescence (root life time) \(\mathrm{degree\ days}\)
deshydbase rate of change of water content in fruits (FW) vs thermal time (>0 or <0) \(\mathrm{g\ g^{-1}\ degree\ days^{-1}}\)
dfolbas minimal foliar density within the considered shape \(\mathrm{m^{2}\ m^{-3}}\)
dfolhaut maximal foliar density within the considered shape \(\mathrm{m^{2}\ m^{-3}}\)
dfpf parameter of the first potential growth phase of fruit, corresponding to an exponential type function describing the cell division phase \(\mathrm{ND}\)
dlaimax maximum rate of net daily increase of LAI \(\mathrm{m^{2}\ pl^{-1}\ degree\ days^{-1}}\)
dlaimaxbrut maximum rate of gross daily increase of LAI \(\mathrm{m^{2}\ pl^{-1}\ degree\ days^{-1}}\)
dlaimin accelerating parameter for the lai growth rate \(\mathrm{ND}\)
dltamsmaxsen growth rate above which there is no more photoperiodic effect on senescence \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
dltamsminsen growth rate below which the photoperiodic effect on senescence is maximal \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
draclong maximum rate of root length production per plant \(\mathrm{cm\ pl^{-1}\ degree\ days^{-1}}\)
dureefruit duration of the fruit between onset and physiological maturity \(\mathrm{degree\ days}\)
durvieF maximal lifespan of an adult leaf expressed in summation of Q10=2 (2**(T-Tbase)) \(\mathrm{ND}\)
durviesupmax relative additional lifespan due to N excess in plant (INN > 1) \(\mathrm{ND}\)
efcroijuv maximum radiation use efficiency during the juvenile phase (LEV-AMF) \(\mathrm{g\ MJ^{-1}}\)
efcroirepro maximum radiation use efficiency during the grain filling phase (DRP-MAT) \(\mathrm{g\ MJ^{-1}}\)
efcroiveg maximum radiation use efficiency during the vegetative stage (AMF-DRP) \(\mathrm{g\ MJ^{-1}}\)
efremobil Efficiency of use of carbohydrates in storage organs of perennials \(\mathrm{ND}\)
elmax maximum elongation of the coleoptile in darkness condition \(\mathrm{cm}\)
envfruit fraction of envelop in grainmaxi \(\mathrm{ND}\)
extin extinction coefficient of photosynthetic active radiation in the canopy \(\mathrm{ND}\)
fixmax maximal N symbiotic fixation rate \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
fixmaxgr maximal N symbiotic fixation rate per unit of grain growth rate \(\mathrm{kg\ t^{-1}}\)
fixmaxveg maximal N symbiotic fixation rate per unit of vegetative growth rate \(\mathrm{kg\ t^{-1}}\)
forme option to define the shape of leaf density profile: 1 = rectangle, 2 = triangle \(\mathrm{code,\ 1\ to\ 2}\)
h2ofeuiljaune water content of yellow leaves (FW) \(\mathrm{g\ g^{-1}}\)
h2ofeuilverte water content of green leaves (FW) \(\mathrm{g\ g^{-1}}\)
h2ofrvert water content of fruits before the beginning of dehydration (FW) \(\mathrm{g\ g^{-1}}\)
h2oreserve water content of crop reserve (FW) \(\mathrm{g\ g^{-1}}\)
h2otigestruc water content of structural stem part (FW) \(\mathrm{g\ g^{-1}}\)
hautbase basal height of crop \(\mathrm{m}\)
hautmax maximum height of crop \(\mathrm{m}\)
idebdorm day of the dormancy entrance \(\mathrm{julian\ day}\)
ifindorm day of dormancy break \(\mathrm{julian\ day}\)
inflomax maximal number of inflorescences per plant \(\mathrm{ND}\)
infrecouv ulai at the stage AMF (maximal rate of leaf growth) \(\mathrm{ND}\)
inilai initial value of lai for cotyledons \(\mathrm{m^{2}\ m^{-2}}\)
inngrain1 NNI below which net absorption of N during grain filling is maximal \(\mathrm{ND}\)
inngrain2 NNI above which net absorption of N during grain filling is nil \(\mathrm{ND}\)
INNimin INNI (instantaneous NNI) corresponding to INNmin \(\mathrm{ND}\)
INNmin minimum value of NNI possible for the crop \(\mathrm{ND}\)
innsen parameter of the N stress function active on senescence (INNsenes) \(\mathrm{ND}\)
innturgmin parameter of the N stress function active on leaf expansion (INNLAI) \(\mathrm{ND}\)
irmax maximum harvest index \(\mathrm{ND}\)
julvernal day of initiation of vernalisation in perennial crops (between 1 and 365) \(\mathrm{julian\ day}\)
jvc number of vernalising days \(\mathrm{days}\)
jvcmini minimum number of vernalising days \(\mathrm{days}\)
kdisrac rate constant defining root length distribution throughout the profile \(\mathrm{cm^{-2}}\)
khaut extinction coefficient connecting LAI to crop height \(\mathrm{ND}\)
Kmabs1 affinity constant of N uptake by roots for the fast uptake system \(\mathrm{micromole\ L^{-1}}\)
Kmabs2 affinity constant of N uptake by roots for the low uptake system \(\mathrm{micromole\ L^{-1}}\)
kmax maximum crop coefficient for water requirements (= MET/PET) \(\mathrm{ND}\)
krepracperm parameter of biomass root partitioning : evolution of the ratio root/total (permanent trophic link) \(\mathrm{ND}\)
krepracseu parameter of biomass root partitioning : evolution of the ratio root/total (trophic link by thresholds) \(\mathrm{ND}\)
kstemflow extinction coefficient connecting LAI to stemflow \(\mathrm{ND}\)
ktrou extinction coefficient of PAR through the crop (used in the radiative transfer module) \(\mathrm{ND}\)
laicomp LAI above which competition between plants starts \(\mathrm{m^{2}\ m^{-2}}\)
laiplantule LAI of plantlet at the plantation \(\mathrm{m^{2}\ m^{-2}}\)
longsperac specific root length \(\mathrm{cm\ g^{-1}}\)
lvfront root density at the root apex \(\mathrm{cm\ cm^{-3}}\)
lvmax maximum root length density in the top soil (used to calculate root mass) \(\mathrm{cm\ cm^{-3}}\)
masecmeta biomass of the plantlet supposed to be composed of metabolic N \(\mathrm{t\ ha^{-1}}\)
masecNmax aerial biomass above which N dilution occurs (critical and maximal curves) \(\mathrm{t\ ha^{-1}}\)
masecplantule initial shoot biomass of plantlet \(\mathrm{t\ ha^{-1}}\)
maxazorac mineral N concentration in soil above which root growth is maximum \(\mathrm{kg\ ha^{-1}\ cm^{-1}}\)
maxtalle maximum tillers density per soil area \(\mathrm{nb\ m^{-2}}\)
minazorac mineral N concentration in soil below which root growth is reduced \(\mathrm{kg\ ha^{-1}\ cm^{-1}}\)
minefnra reduction factor on root growth when soil mineral N is limiting (< minazorac) \(\mathrm{ND}\)
mouillabil maximum wettability of leaves \(\mathrm{mm\ m^{-2}}\)
nbfeuilplant leaf number per plant when planting \(\mathrm{pl^{-1}}\)
nbfgellev leaf number at the end of the juvenile phase (frost sensitivity) \(\mathrm{pl^{-1}}\)
nbgrmax maximum number of fruits per surface area \(\mathrm{m^{-2}}\)
nbgrmin minimum number of fruits per surface area \(\mathrm{m^{-2}}\)
nbinflo imposed number of inflorescences per plant \(\mathrm{pl^{-1}}\)
nbjgerlim maximum number of days after grain imbibition allowing full germination \(\mathrm{days}\)
nbjgrain number of days used to compute the number of viable grains \(\mathrm{days}\)
nboite number of boxes or age classes of fruits used to calculate fruit growth for undeterminate crops \(\mathrm{ND}\)
nlevlim1 number of days after germination after which plant emergence is reduced \(\mathrm{days}\)
nlevlim2 number of days after germination after which plant emergence is impossible \(\mathrm{days}\)
Nmeta proportion of metabolic N in the plantlet \(\mathrm{\%}\)
Nreserve maximal proportion of N in plant reserves (difference between the maximal and critical dilution curves) \(\mathrm{\%}\)
parazofmorte C/N ratio of dead leaves when crop NNI = 1 \(\mathrm{g\ g^{-1}}\)
Parazoper C/N ratio of perennial organs when crop NNI = 1 \(\mathrm{g\ g^{-1}}\)
parazorac C/N ratio of roots when crop NNI = 1 \(\mathrm{g\ g^{-1}}\)
ParazoTmorte C/N ratio of dead stems when crop NNI = 1 \(\mathrm{g\ g^{-1}}\)
pentinflores parameter used to calculate the inflorescences number \(\mathrm{kg^{-1}}\)
pentlaimax parameter of the logistic curve of LAI growth \(\mathrm{ND}\)
pentrecouv parameter of the logistic curve of soil cover rate \(\mathrm{ND}\)
pgrainmaxi maximum grain weight (at 0% water content) \(\mathrm{g}\)
phobase basal photoperiod \(\mathrm{hours}\)
phobasesen photoperiod under which the photoperiodic stress affects the lifespan of leaves \(\mathrm{hours}\)
phosat saturating photoperiod \(\mathrm{hours}\)
phyllotherme thermal duration between the apparition of two successive leaves on the main stem \(\mathrm{degree\ days}\)
potgermi soil water potential below which seed imbibition is impeded \(\mathrm{MPa}\)
profnod maximum depth at which N2 fixation by legume crops is possible \(\mathrm{cm}\)
propjgermin minimal fraction of the duration nbjgerlim when the temperature is higher than the temperature threshold Tdmax \(\mathrm{\%}\)
propracfmax fraction of fine roots emitted in the layer 0-1 cm (in length, maximum value over the root profile) \(\mathrm{ND}\)
Propres maximal fraction of the biomass reserves that can be mobilized from aerial organs in all crops \(\mathrm{ND}\)
propresP maximal fraction of the biomass reserves that can be mobilized from storage organs in perennials \(\mathrm{ND}\)
PropresPN maximal fraction of the N reserves that can be mobilized from storage organs in perennials \(\mathrm{ND}\)
psisto potential of stomatal closing (absolute value) \(\mathrm{bars}\)
psiturg potential of the beginning of decrease of the cellular extension (absolute value) \(\mathrm{bars}\)
q10 Q10 used for the dormancy break calculation \(\mathrm{ND}\)
rapdia ratio of coarse roots diameter to fine roots diameter \(\mathrm{ND}\)
rapforme ratio of thickness to width of the crop shape (negative when the base of the form < top) \(\mathrm{ND}\)
rapsenturg threshold soil water content active to simulate water senescence stress as a proportion of the turgor stress \(\mathrm{ND}\)
ratiodurvieI life span of early leaves expressed as a fraction of the life span of the last leaves emitted DURVIEF \(\mathrm{ND}\)
ratiosen fraction of senescent biomass (relative to total biomass) \(\mathrm{ND}\)
rayon average radius of the roots \(\mathrm{cm}\)
remobres fraction of daily remobilisable C reserves \(\mathrm{day^{-1}}\)
repracpermax maximum root biomass relative to total biomass (permanent trophic link) \(\mathrm{ND}\)
repracpermin minimum root biomass relative to total biomass (permanent trophic link) \(\mathrm{ND}\)
repracseumax maximum root biomass relative to total biomass (trophic link by thresholds) \(\mathrm{ND}\)
repracseumin minimum root biomass relative to total biomass (trophic link by thresholds) \(\mathrm{ND}\)
resplmax maximal reserve of biomass \(\mathrm{t\ ha^{-1}}\)
rsmin minimal stomatal resistance of leaves \(\mathrm{s\ m^{-1}}\)
RTD root tissue density \(\mathrm{g\ cm^{-3}}\)
sea specific area of fruit envelops \(\mathrm{cm^{2}\ g^{-1}}\)
sensanox index of anoxia sensitivity (0 = insensitive, 1 = highly sensitive) \(\mathrm{ND}\)
sensiphot index of photoperiod sensitivity (1 = insensitive, 0 = highly sensitive) \(\mathrm{ND}\)
sensrsec index of root sensitivity to drought (1 = insensitive, 0 = highly sensitive) \(\mathrm{ND}\)
seuilLAIapex maximal value of LAI+LAIapex when LAIapex is > 0 \(\mathrm{m^{2}\ m^{-2}}\)
seuilmortalle relative transpiration threshold to calculate tiller mortality \(\mathrm{mm\ day^{-1}}\)
seuilreconspeupl tiller density below which the entire population will not be regenerated \(\mathrm{m^{-2}}\)
sigmadistalle parameter used for calculating tiller mortality (gamma law) \(\mathrm{ND}\)
slamax maximum SLA (specific leaf area) of green leaves \(\mathrm{cm^{2}\ g^{-1}}\)
slamin minimum SLA (specific leaf area) of green leaves \(\mathrm{cm^{2}\ g^{-1}}\)
spfrmax maximal sources/sinks value allowing the trophic stress calculation for fruit onset \(\mathrm{ND}\)
spfrmin minimal sources/sinks value allowing the trophic stress calculation for fruit onset \(\mathrm{ND}\)
splaimax maximal sources/sinks value allowing the trophic stress calculation for leaf growing \(\mathrm{ND}\)
splaimin minimal value of ratio sources/sinks for the leaf growth \(\mathrm{ND}\)
stadebbchamf equivalent stage in BBCH-scale (amf= maximum acceleration of leaf growth, end of juvenile phase) \(\mathrm{ND}\)
stadebbchdebdes equivalent stage in BBCH-scale (debdes= date of onset of water dynamics in harvested organs) \(\mathrm{ND}\)
stadebbchdrp equivalent stage in BBCH-scale (drp = starting date of filling of harvested organs) \(\mathrm{ND}\)
stadebbchfindorm equivalent stage in BBCH-scale (end of dormancy) \(\mathrm{ND}\)
stadebbchflo equivalent stage in BBCH-scale (flowering) \(\mathrm{ND}\)
stadebbchger equivalent stage in BBCH-scale (germination) \(\mathrm{ND}\)
stadebbchlax equivalent stage in BBCH-scale (lax = maximum leaf area index, end of leaf growth ) \(\mathrm{ND}\)
stadebbchlev equivalent stage in BBCH-scale (emergence) \(\mathrm{ND}\)
stadebbchmat equivalent stage in BBCH-scale (maturity) \(\mathrm{ND}\)
stadebbchnou equivalent stage in BBCH-scale (fruit set) \(\mathrm{ND}\)
stadebbchplt equivalent stage in BBCH-scale (sowing) \(\mathrm{ND}\)
stadebbchrec equivalent stage in BBCH-scale (harvest) \(\mathrm{ND}\)
stadebbchsen equivalent stage in BBCH-scale (senescence) \(\mathrm{ND}\)
stamflax cumulative thermal time between the stages AMF (maximum acceleration of leaf growth, end of juvenile phase) and LAX (maximum leaf area index, end of leaf growth ) \(\mathrm{degree\ days}\)
stdnofno cumulative thermal time between the beginning and the end of nodulation \(\mathrm{degree\ days}\)
stdordebour cumulative thermal time between the dormancy break and the bud break \(\mathrm{degree\ days}\)
stdrpdes cumulative thermal time between the DRP stage (starting date of filling of harvested organs) and DEBDES (date of onset of water dynamics in harvested organs) \(\mathrm{degree\ days}\)
stdrpmat cumulative thermal time between the stages DRP (starting date of filling of harvested organs) and MAT (maturity) \(\mathrm{degree\ days}\)
stdrpnou cumulative thermal time between the stages DRP (starting date of filling of harvested organs) and NOU (end of setting) \(\mathrm{degree\ days}\)
stemflowmax maximal fraction of rainfall flowing down along the stems \(\mathrm{ND}\)
stflodrp cumulative thermal time between FLO (anthesis) and DRP (starting date of filling of harvested organs) (only for indication) \(\mathrm{degree\ days}\)
stfnofvino cumulative thermal time between the end of the nodulation and the end of the nodule life \(\mathrm{degree\ days}\)
stlaxsen cumulative thermal time between the stages LAX (maximum leaf area index, end of leaf growth ) and SEN (beginning of leaf senescence) \(\mathrm{degree\ days}\)
stlevamf cumulative thermal time between the stages LEV (emergence) and AMF (maximum acceleration of leaf growth, end of juvenile phase) \(\mathrm{degree\ days}\)
stlevdno cumulative thermal time between emergence and the beginning of nodulation \(\mathrm{degree\ days}\)
stlevdrp cumulative thermal time between the stages LEV (emergence) and DRP (starting date of filling of harvested organs) \(\mathrm{degree\ days}\)
stoprac stage when root growth stops (LAX= maximum leaf area index, end of leaf growth or SEN=beginning of leaf senescence) \(\mathrm{ND}\)
stpltger cumulative thermal time allowing germination \(\mathrm{degree\ days}\)
stressdev maximum phasic delay allowed due to stresses \(\mathrm{ND}\)
stsenlan cumulative thermal time between the stages SEN (beginning of leaf senescence) and LAN \(\mathrm{degree\ days}\)
surfapex equivalent surface of a transpiring apex \(\mathrm{m^{2}}\)
swfacmin minimal value for drought stress index (turfac, swfac, senfac) \(\mathrm{ND}\)
tauxmortresP mortality rate of perennial organs \(\mathrm{day^{-1}}\)
tauxrecouvkmax soil cover rate corresponding to the maximal crop coefficient for water requirement (plant surface / soil surface) \(\mathrm{m^{2}\ m^{-2}}\)
tauxrecouvmax maximal soil cover rate (plant surface / soil surface) \(\mathrm{m^{2}\ m^{-2}}\)
tcmax maximum temperature at which growth ceases \(\mathrm{^{\circ}C}\)
tcmin minimum temperature at which growth ceases \(\mathrm{^{\circ}C}\)
tcxstop temperature beyond which foliar growth stops \(\mathrm{^{\circ}C}\)
tdebgel temperature below which frost affects plant growth \(\mathrm{^{\circ}C}\)
tdmax maximum temperature above which development stops \(\mathrm{^{\circ}C}\)
tdmaxdeb maximal temperature for hourly calculation of phasic duration between dormancy and bud breaks \(\mathrm{^{\circ}C}\)
tdmin minimum temperature below which development stops \(\mathrm{^{\circ}C}\)
tdmindeb minimal thermal threshold for hourly calculation of phasic duration between dormancy and bud breaks \(\mathrm{^{\circ}C}\)
tdoptdeb optimal temperature for calculation of phasic duration between dormancy and bud breaks \(\mathrm{^{\circ}C}\)
temax maximal temperature above which plant growth stops \(\mathrm{^{\circ}C}\)
temin minimum temperature for development \(\mathrm{^{\circ}C}\)
tempdeshyd increase in fruit dehydration rate due to the increase in crop temperature (Tcult-Tair) \(\mathrm{\%\ ^{\circ}C^{-1}}\)
tempnod1 temperature parameter (1/4) used to calculate N fixation by legumes \(\mathrm{^{\circ}C}\)
tempnod2 temperature parameter (2/4) used to calculate N fixation by legumes \(\mathrm{^{\circ}C}\)
tempnod3 temperature parameter (3/4) used to calculate N fixation by legumes \(\mathrm{^{\circ}C}\)
tempnod4 temperature parameter (4/4) used to calculate N fixation by legumes \(\mathrm{^{\circ}C}\)
teopt optimal temperature (1/2) for plant growth \(\mathrm{^{\circ}C}\)
teoptbis optimal temperature (2/2) for plant growth \(\mathrm{^{\circ}C}\)
tfroid optimal temperature for vernalisation \(\mathrm{^{\circ}C}\)
tgelflo10 temperature resulting in 10% of frost damages on flowers and fruits \(\mathrm{^{\circ}C}\)
tgelflo90 temperature resulting in 90% of frost damages on flowers and fruits \(\mathrm{^{\circ}C}\)
tgeljuv10 temperature resulting in 10% of frost damage on LAI (juvenile stage) \(\mathrm{^{\circ}C}\)
tgeljuv90 temperature resulting in 90% of frost damage on LAI (juvenile stage) \(\mathrm{^{\circ}C}\)
tgellev10 temperature resulting in 10% of frost damages on plantlet \(\mathrm{^{\circ}C}\)
tgellev90 temperature resulting in 90% of frost damages on plantlet \(\mathrm{^{\circ}C}\)
tgelveg10 temperature resulting in 10% of frost damage on LAI (adult stage) \(\mathrm{^{\circ}C}\)
tgelveg90 temperature resulting in 90% of frost damage on LAI (adult stage) \(\mathrm{^{\circ}C}\)
tgmin minimum temperature below which emergence is stopped \(\mathrm{^{\circ}C}\)
tigefeuil ratio stem (structural part)/leaf \(\mathrm{ND}\)
tigefeuilcoupe ratio stem (structural part)/leaf on the cutting day \(\mathrm{ND}\)
tletale lethal temperature for the plant \(\mathrm{^{\circ}C}\)
tmaxremp maximal temperature above which grain filling stops \(\mathrm{^{\circ}C}\)
tminremp minimal temperature below which grain filling stops \(\mathrm{^{\circ}C}\)
tustressmin water stress index (min(turfac,inns)) below which there is an extra LAI senescence \(\mathrm{ND}\)
udlaimax ulai from which the rate of leaf growth decreases \(\mathrm{ND}\)
vigueurbat plant vigor index allowing to emerge through a soil crust \(\mathrm{ND}\)
vitirazo rate of increase of the N harvest index vs time \(\mathrm{g\ g^{-1}\ day^{-1}}\)
vitircarb rate of increase of the C harvest index vs time \(\mathrm{g\ g^{-1}\ day^{-1}}\)
vitircarbT rate of increase of the C harvest index vs thermal time \(\mathrm{g\ g^{-1}\ degree\ days^{-1}}\)
vitno rate of increase of the potential biological fixation rate after nodule onset, per unit of thermal time \(\mathrm{nb\ degree\ days^{-1}}\)
vitprophuile rate of increase of oil harvest index vs time \(\mathrm{g\ g^{-1}\ day^{-1}}\)
vitpropsucre rate of increase of sugar harvest index vs time \(\mathrm{g\ sugar\ g^{-1}\ day^{-1}}\)
vitreconspeupl rate of regeneration of the tiller population \(\mathrm{^{\circ}C^{-1}}\)
vlaimax ulai at the inflexion point of the function DELTAI=f(ULAI) \(\mathrm{ND}\)
Vmax1 maximum specific N uptake rate with the low affinity transport system \(\mathrm{micromole\ cm^{-1}\ h^{-1}}\)
Vmax2 maximum specific N uptake rate with the high affinity transport system \(\mathrm{micromole\ cm^{-1}\ h^{-1}}\)
zlabour depth of ploughing (reference profile) \(\mathrm{cm}\)
zpente depth at which root density is 50% of the surface root density (reference profile) \(\mathrm{cm}\)
zprlim maximum depth of the root profile (reference profile) \(\mathrm{cm}\)
zracplantule initial depth of root apex of the plantlet \(\mathrm{cm}\)

3.3.2 Local parameters

To view or edit the local parameters files, choose Model inputs/Local parameters.

Local parameters

Figure 3.4: Local parameters

The local parameters include five sets of files corresponding to:

  • Initialisation of the system at simulation start

  • Soils parameters

  • Crop management parameters

  • Climate inputs including wheather data and station parameters

3.3.2.1 Initialisation parameters

The initialisation file follows the naming convention *_ini.xml. It is located in the workspace directory. It provides the initial state of the system at the simulation start.

Choose Model inputs/Local parameters/initialisations, and then click Open to select an initialisation file and click Open again. In a newly created workspace directory, you will find the default example file called mais_ini.xml.

The initialisation parameters are presented in separate tabs corresponding to four parameters groups:

  • The first tab corresponds to the initialisation parameters for the main crop: development stage, plant state description and roots densities in layers.

  • The second tab corresponds to the initialisation parameters for the associated crop, if there’s any (check the box near tab title, if you are using associated crops)

  • The third tab corresponds to the initial soil water and nitrogen content

  • The fourth tab corresponds to the initial snow state variables values

Simply change the values in the corresponding boxes, then save the changes by clicking Save or Save as for creating a new file.

Plant initialisation

Figure 3.5: Plant initialisation

Even if the simulation starts with a bare soil, the plant and roots initialisation parameters must be filled with zeros.

The starting stages are described in the following table:

Table 3.4: List of the phenological stages of STICS
Name Definition Phase
SNU bare soil vegetative
PLT sowing or planting (annuals) vegetative
LEV emergence or budding vegetative
DOR beginning of dormancy (woody plants) vegetative
AMF maximum acceleration of leaf growth, end of juvenile phase vegetative
DRP onset of filling of harvested organs reproductive
LAX maximum leaf area index, end of leaf growth vegetative
SEN beginning of net senescence (LAInet option) vegetative
Table 3.5: Table of parameters (Plants and roots) contained in initialisation files
Name Definition Unit
densinitial initial root density in each of the five soil layers \(\mathrm{cm\ cm^{-3}}\)
lai0 initial leaf area index \(\mathrm{m^{2}\ m^{-2}}\)
magrain0 initial grain dry weight \(\mathrm{g\ m^{-2}}\)
maperenne0 initial value of biomass of storage organs in perennial crops \(\mathrm{t\ ha^{-1}}\)
masec0 initial plant biomass (if the option to simulate N and C reserves is not activated) \(\mathrm{t\ ha^{-1}}\)
masecnp0 initial aerial biomass \(\mathrm{t\ ha^{-1}}\)
QNperenne0 initial value of nitrogen amount in storage organs in perennial crops \(\mathrm{kg\ ha^{-1}}\)
QNplante0 initial N amount in the plant (if the option to simulate N and C reserves is not activated) \(\mathrm{t\ ha^{-1}}\)
QNplantenp0 initial N amount in non-perennial organs of the plant \(\mathrm{kg\ ha^{-1}}\)
restemp0 initial biomass of metabolic reserves in the perennial organs \(\mathrm{t\ ha^{-1}}\)
stade0 crop stage at the beginning of simulation \(\mathrm{ND}\)
zrac0 initial depth of root apex of the crop \(\mathrm{cm}\)
Soil initialisation

Figure 3.6: Soil initialisation

Table 3.6: Table of soil parameters contained in initialisation files
Name Definition Unit Warnings
Hinitf initial gravimetric water content of each soil layer (in fine earth, dry soil) \(\mathrm{\%}\) Hinitf = 0 is a code meaning hinit = hccf (field capacity)
NH4initf initial amount of NH4-N in each of the soil layers (in fine earth) \(\mathrm{kg\ ha^{-1}}\)
NO3initf initial amount of NO3-N in each of the soil layers (in fine earth) \(\mathrm{kg\ ha^{-1}}\)

The whole table must be filled in, even if the soil is described with less than 5 layers. If the soil has less than 5 layers, then put a value of zero for the parameters of the layers not present in the soil.

The NH4initf parameters are used by the model only if nitrification is activated (see the parameter codenitrif of the soil parameterisation). If nitrification is not activated, then put NH4initf to zero for all layers.

TODO: remplacer l’image du tab de snow pour être homogène avec le reste

Snow initialisation

Figure 3.7: Snow initialisation

Table 3.7: Table of snow parameters contained in initialisation files
Name Definition Unit
ps0 initial density of the snow cover \(\mathrm{kg\ m^{-3}}\)
Sdepth0 initial snow cover depth \(\mathrm{m}\)
Sdry0 initial water in solid state in the snow cover \(\mathrm{mm}\)
Swet0 initial water in liquid state in the snow cover \(\mathrm{mm}\)

3.3.2.2 Soil parameters

The sols.xml file contains parameters of all soils used in a workspace directory.

Choose menu Model inputs/Local parameters/Soils. In a newly created working directory, a default sols.xml file has been created. It contains a single soil.

In the view window, the soil parameters appear in the form of a tree structure whose branches can be expanded by clicking on icons beside each soil name.

There are two types of parameters:

  • options parameters: in this case, a drop-down list shows the different possible values that can be selected inside an option.

  • parameters to which a value must be set: in this case the value is entered in the input field beside the parameter name. The icon on the right, when clicked opens a popup containing information on the parameter: description, type (numeric or alphanumeric), unit, boundaries values.

To add a new soil, click the Add button; enter its name (without any spaces). By default, its parameters are filled with the values of the first soil of the list if no soil was selected or of selected soil (after clicking on its name). A confirm popup indicates from with soil parameters the new one will be added.

To delete a soil, select a soil by clicking on its name and then click Remove.

Click the Save button to save your changes.

Soil parameter file

Figure 3.8: Soil parameter file

A complete list of soil parameters is given in the table below.

Table 3.8: Table of parameters contained in the soils.xml file
Name Definition Unit
albedo albedo of the bare dry soil \(\mathrm{ND}\)
argi clay content after decarbonation \(\mathrm{\%}\)
cailloux volumetric content of pebbles per soil layer \(\mathrm{\%}\)
calc total carbonate content \(\mathrm{\%}\)
capiljour capillary rise upward water flux \(\mathrm{mm\ day^{-1}}\)
cfes parameter defining the soil contribution to evaporation versus depth \(\mathrm{ND}\)
codecailloux option to take into account pebbles in the water and N balances: 1 = yes, 2 = no \(\mathrm{code,\ 0\ to\ 1}\)
codedenit option to activate the calculation of denitrification model: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codefente option to activate an additional water compartment for swelling soils: 1 = yes, 2 = no \(\mathrm{code,\ 0\ to\ 1}\)
codemacropor option to activate calculation of water flux in soil macroporosity: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codenitrif option to activate the nitrification model: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
coderemontcap option to activate capillary rise: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codrainage option to simulate artificial drainage: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
concseuil minimum concentration of NO3-N in soil (unavailable for leaching and for uptake) \(\mathrm{kg\ ha^{-1}\ mm^{-1}}\)
CsurNsol C to N ratio of soil humus \(\mathrm{g\ g^{-1}}\)
DAF bulk density of fine earth fraction in each soil layer \(\mathrm{g\ cm^{-3}}\)
ecartdrain distance between mole drains \(\mathrm{cm}\)
epc thickness of each soil layer \(\mathrm{cm}\)
epd thickness of mixing cells in each soil layer ( = 2 * dispersion length) \(\mathrm{cm}\)
finert initial fraction of inert pool in the soil organic pool (= stable SON/ total SON) \(\mathrm{ND}\)
hccf gravimetric water content at field capacity of each soil layer (in fine earth, dry soil) \(\mathrm{\%}\)
hminf gravimetric water content at wilting point of each soil layer (in fine earth, dry soil) \(\mathrm{\%}\)
humcapil threshold of soil gravimetric water content under which capillary rise occurs (dry soil) \(\mathrm{\%}\)
infil infiltrability rate at the base of each soil layer (if codemacropor = 1) \(\mathrm{mm\ day^{-1}}\)
ksol soil hydraulic conductivity in the vicinity of mole drains \(\mathrm{ND}\)
mulchbat mulch depth at which a crust occurs (a value must be given but if in the plt.xml the vigueurbat parameter is equal to 1 then the parameter is inactive) \(\mathrm{cm}\)
Norg soil organic N content in the first soil layer (constant down to the depth profhum, dry soil) \(\mathrm{\%}\)
obstarac soil depth at which root growth is stopped due to physical constraints \(\mathrm{cm}\)
penterui runoff coefficient taking into account the plant mulch \(\mathrm{ND}\)
pH0 Initial soil pH (water solution) \(\mathrm{pH}\)
pluiebat minimal amount of rain required to create a soil crust (a value must be given but if in the plt.xml the vigueurbat parameter is equal to 1 then the parameter is inactive) \(\mathrm{mm\ day^{-1}}\)
profdenit soil depth at which denitrification is active (if codedenit is activated) \(\mathrm{cm}\)
profdrain depth of mole drains \(\mathrm{cm}\)
profhum maximum soil depth with an active biological activity \(\mathrm{cm}\)
profimper upper depth of the impermeable layer (from the soil surface) \(\mathrm{cm}\)
q0 cumulative soil evaporation above which evaporation rate is decreased \(\mathrm{mm}\)
ruisolnu fraction of runoff (relative to total rainfall) in a bare soil \(\mathrm{ND}\)
typecailloux Pebbles type: 1 = Beauce limestone1, 2 = Beauce limestone, 3 = Lutetian limestone, 4 = Lutetian Brackish marl and limestone, 5 = morainic gravels, 6 = unweathered flint, sandstone or granite, 7 = weathered granite, 8 = Jurassic limestone 9 = Pebbles from Magneraud \(\mathrm{ND}\)
typsol soil type \(\mathrm{ND}\)
vpotdenit potential rate of denitrification for the whole denitrifying layer \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
z0solnu roughness length of bare soil \(\mathrm{m}\)
zesx maximal soil depth affected by soil evaporation \(\mathrm{cm}\)

3.3.2.3 Crop management parameters

The crop management file follows the naming convention *_tec.xml. It is located in the workspace directory.

Choose Model inputs menu/Local parameters/Crop management. In a newly created working directory, a default Mais_tec.xml file has been created.

To create a new crop management parameter file, select the crop management file you want to use as model in the drop-box list, click on New file and enter the prefix of the new file, and click OK. A new crop management file is created using the crop management file previously selected.

To edit or view the crop management file, select the file to view, then click Open.

crop management file selection

Figure 3.9: crop management file selection

crop management editing

Figure 3.10: crop management editing

The options and their parameters can be expanded or closed in the tree structure by clicking on the icon left to items.

The table below lists the crop management parameters:

Table 3.9: Table of parameters contained in the crop_management.xml file
Name Definition Unit
albedomulchplastique albedo of plastic cover \(\mathrm{ND}\)
anitcoupe amount of mineral N added by fertiliser application at each cut of a forage crop \(\mathrm{kg\ ha^{-1}}\)
biorognem minimal crop biomass removed when topping (automatic calculation) \(\mathrm{t\ ha^{-1}}\)
cadencerec number of days between two harvests \(\mathrm{days}\)
CNgrainrec minimal N content of grain at harvest \(\mathrm{g\ g^{-1}}\)
codabri option to activate cropping under shelter: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codcaleffeuil option to calculate leaf removal by thinning: 1 = proportion of leaf removed (effeuil), 2 = lai minimal (laieffeuil) \(\mathrm{code,\ 1\ to\ 2}\)
codcalrogne option to calculate topping: 1 = forced topping, 2 = automatic calculation \(\mathrm{code,\ 1\ to\ 2}\)
codcueille option to define harvest type: 1 =single harvest (cutting), 2 = multiple harvests (picking) \(\mathrm{code,\ 1\ to\ 2}\)
code_auto_profres option to define profres: 1 = profres read in tec file, 2 = profres calculated as proftrav *(1-exp(-resk.(proftrav-resz)) \(\mathrm{code,\ 1\ to\ 2}\)
code_hautfauche_dyn option to activate dynamic calculation of residual LAI, biomass and N content after cutting: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeaumin option to activate the harvest according to grain/fruit water content: 1 = water content > minimum threshold, 2 = water content < maximum threshold \(\mathrm{code,\ 1\ to\ 2}\)
codecalirrig option to activate the automatic calculation of irrigation requirements: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeclaircie option to simulate fruit removal: 1 = no, 2 = yes (for smallest fruits) \(\mathrm{code,\ 1\ to\ 2}\)
codedate_irrigauto option to activate the beginning and the ending dates in case of automatic irrigation: 1 = dates, 2= crop stages, 3 = nothing \(\mathrm{code,\ 1\ to\ 3}\)
codedateappH2O option to calculate irrigation dates according to sum of temperatures: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codedateappN option to calculate mineral fertilizer application dates according to sum of temperatures: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codedecirecolte option to activate moisture and frost effects on harvest decision: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codedecisemis option to activate the moisture effect on harvest decision: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeDST option to activate the variations in physical soil conditions due to tillage: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeDSTnbcouche option to define the number of compacted soil layers: 1 = one layer, 2 = two layers \(\mathrm{code,\ 1\ to\ 2}\)
codeDSTtass option to activate the soil compaction at sowing and harvest: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codefauche option to activate cuts of forage crops: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codeffeuil option to activate plant thinning: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codefracappN option to activate split applications of N fertiliser: 1 = absolute value, 2 = fraction of total N application \(\mathrm{code,\ 1\ to\ 2}\)
codejourdes option to simulate perennial crops destruction \(\mathrm{code,\ 1\ to\ 2}\)
codemodfauche option to define the cutting mode: 1 = automatic calculation depending on phenologic and trophic state, 2 = pre-established calendar in days, 3 = pre-established calendar in degree-days \(\mathrm{code,\ 1\ to\ 3}\)
codepaillage option to define soil cover: 1 = no cover, 2 = plastic cover partly covering the soil \(\mathrm{code,\ 1\ to\ 2}\)
codepalissage option to define if the plant is fixed onto a vertical support: 1 = no, 2 =yes \(\mathrm{code,\ 1\ to\ 2}\)
coderecolteassoc option to harvest intercrop species simultaneously, at the physiological maturity date of the earliest one: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
coderes residue type: 1=mature crop, 2=cover crop, 3=Manure, 4=Green compost, 5=Sewage sludge, 6=Vinasse, 7=Horn, 8=vineyard prunings, 9=pig slurry, 10=rhizomes \(\mathrm{code,\ 1\ to\ 10}\)
codestade option to force one or several development stages: 1 = yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codetaille option to activate pruning: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codetempfauche option to define the reference temperature to compute cutting sum of temperatures: 1 = upvt, 2 = udevair \(\mathrm{code,\ 1\ to\ 2}\)
codetradtec option to activate the effect of crop structure on radiation transfer: 1 =yes, 2 = no \(\mathrm{code,\ 1\ to\ 2}\)
codhauteff option to define the height of leaf removal (if the thinning option is activated): 1 = bottom of the canopy, 2 = top of the canopy \(\mathrm{code,\ 1\ to\ 2}\)
codlocferti option to define localized fertilisation: 1 = at soil surface, 2 = deeper in the soil \(\mathrm{code,\ 1\ to\ 2}\)
codlocirrig option to define localized irrigation: 1= above the foliage, 2= below the foliage above the soil, 3 = in the soil \(\mathrm{code,\ 1\ to\ 3}\)
codrecolte option to define harvest strategy: 1 = at physiological maturity, 2 = according to water content, 3 = according to sugar content, 4 = according to nitrogen content, 5 = according to oil content \(\mathrm{code,\ 1\ to\ 5}\)
codrognage option to activate foliage control by trimming: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
concirr concentration of mineral N (NH4+NO3-N) in irrigation water \(\mathrm{kg\ ha^{-1}\ mm^{-1}}\)
couvermulchplastique fraction of soil covered by the plastic mulch \(\mathrm{ND}\)
Crespc C content in organic residue (FW) \(\mathrm{\%}\)
CsurNres C/N ratio of residue \(\mathrm{g\ g^{-1}}\)
dachisel bulk density of soil after soil tillage (Chisel) \(\mathrm{g\ cm^{-3}}\)
dalabour bulk density of soil after full inversion tillage (plough) \(\mathrm{g\ cm^{-3}}\)
darecolte bulk density of soil after harvest \(\mathrm{g\ cm^{-3}}\)
dasemis bulk density of soil after sowing \(\mathrm{g\ cm^{-3}}\)
datedeb_irrigauto starting date of automatic irrigations \(\mathrm{julian\ day}\)
datefin_irrigauto ending date of automatic irrigations \(\mathrm{julian\ day}\)
densitesem plant sowing density \(\mathrm{pl\ m^{-2}}\)
doseI daily amount of irrigation water \(\mathrm{mm\ day^{-1}}\)
doseirrigmin minimal amount of daily irrigation \(\mathrm{mm\ day^{-1}}\)
doseN daily amount of N added through fertilizers \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
dosimx maximum amount of irrigation water applied daily (mode automatic irrigation) \(\mathrm{mm\ day^{-1}}\)
eau_mini_decisemis minimum amount of rainfall required to start sowing (when codesemis is activated) \(\mathrm{mm}\)
eaures water content of organic residue (FW) \(\mathrm{\%}\)
effeuil fraction of leaf removed by plant thinning \(\mathrm{ND}\)
effirr irrigation efficiency \(\mathrm{ND}\)
engrais fertilizer type (1=ammonium nitrate, 2=UAN solution, 3=urea, 4=anhydrous ammonia, 5=ammonium sulfate, 6=ammonium phosphate, 7=calcium nitrate, 8= fixed efficiency fertiliser) \(\mathrm{ND}\)
engraiscoupe fertilizer type (1=ammonium nitrate, 2=UAN solution, 3=urea, 4=anhydrous ammonia, 5=ammonium sulfate, 6=ammonium phosphate, 7=calcium nitrate, 8= fixed efficiency fertiliser) \(\mathrm{ND}\)
fracN proportion of fertiliser N applied at each application \(\mathrm{\%}\)
h2ograinmax maximal water content of fruits at harvest (FW) \(\mathrm{g\ g^{-1}}\)
h2ograinmin minimal water content of fruits at harvest (FW) \(\mathrm{g\ g^{-1}}\)
hautcoupe cut height for forage crops (calendar fixed) \(\mathrm{m}\)
hautcoupedefaut cut height for forage crops (calendar calculated) \(\mathrm{m}\)
hautmaxtec maximal height of the plant allowed by the management \(\mathrm{m}\)
hautrogne cutting height for trimmed plants \(\mathrm{m}\)
huilerec minimal oil content of fruits at harvest (FW) \(\mathrm{g\ g^{-1}}\)
humirac_decisemis relative soil moisture threshold above which sowing is possible (0 = no sensitivity to drought, 1 = highly sensitive) \(\mathrm{ND}\)
iamf day when the stage AMF is reached (999 if not reached) \(\mathrm{julian\ day}\)
idrp day of the stage DRP (beginning of grain filling) when the stage is observed (else 999) \(\mathrm{julian\ day}\)
iflo day of anthesis \(\mathrm{julian\ day}\)
ilan day when the stage LAN is reached (999 if not observed) \(\mathrm{julian\ day}\)
ilax day when the stage LAX is reached (999 if not observed) \(\mathrm{julian\ day}\)
ilev day when the stage LEV is reached (999 if not observed) \(\mathrm{julian\ day}\)
imat day when the stage MAT is reached (999 if not observed) \(\mathrm{julian\ day}\)
interrang width of the crop interrow \(\mathrm{m}\)
iplt0 date of sowing \(\mathrm{julian\ day}\)
irec date of harvest \(\mathrm{julian\ day}\)
irecbutoir latest date of harvest (imposed if the crop cycle is not finished at this date) \(\mathrm{julian\ day}\)
isen day when the stage SEN is reached (999 if not observed) \(\mathrm{julian\ day}\)
julapI date(s) of irrigation \(\mathrm{julian\ day}\)
julapN date(s) of fertilizer application \(\mathrm{julian\ day}\)
juldes day of perennial crop destruction \(\mathrm{julian\ day}\)
juleclair day of fruits removal \(\mathrm{julian\ day}\)
juleffeuil day of leaf removal \(\mathrm{julian\ day}\)
julfauche date(s) of each cut for forage crops \(\mathrm{julian\ day}\)
julouvre2 day (1/2) of opening the shelter \(\mathrm{julian\ day}\)
julouvre3 day (2/2) of opening the shelter \(\mathrm{julian\ day}\)
julres date(s) of organic residue addition to soil \(\mathrm{julian\ day}\)
julrogne day of plant trimming \(\mathrm{julian\ day}\)
jultaille day of pruning \(\mathrm{julian\ day}\)
jultrav date(s) of soil tillage \(\mathrm{julian\ day}\)
laidebeff LAI at the beginning of leaf removal \(\mathrm{m^{2}\ m^{-2}}\)
laieffeuil LAI removed from the crop at day juleffeuil \(\mathrm{m^{2}\ m^{-2}}\)
lairesiduel residual LAI after each cut of forage crop \(\mathrm{m^{2}\ m^{-2}}\)
largrogne trimmed width \(\mathrm{m}\)
largtec technical width \(\mathrm{m}\)
locferti soil depth at which fertiliser is applied \(\mathrm{cm}\)
locirrig soil depth at which irrigation is applied \(\mathrm{cm}\)
margerogne topping occurs when plant height exceeds (hautrogne+margerogne) when automatic trimming is activated \(\mathrm{m}\)
mscoupemini minimum value of aerial biomass required to make a cut of forage crop \(\mathrm{t\ ha^{-1}}\)
msresiduel residual aerial biomass after a cut of a forage crop \(\mathrm{t\ ha^{-1}}\)
nbcueille number of fruit harvests during the crop cycle: 1 = one harvest, 2 = several harvests \(\mathrm{code,\ 1\ to\ 2}\)
nbinfloecl number of inflorescences or fruits removed at fruit removal \(\mathrm{pl^{-1}}\)
nbj_pr_apres_semis number of days used to calculate rainfall requirement to start sowing (if codesemis is activated) \(\mathrm{days}\)
nbjmaxapresrecolte maximum number of days allowed for harvest (if the soil compaction option is activated) \(\mathrm{days}\)
nbjmaxapressemis maximum number of days allowed for sowing (if the soil compaction option is activated) \(\mathrm{days}\)
nbjres number of residue additions \(\mathrm{ND}\)
nbjseuiltempref number of days without frost for sowing (if sowing decision option is activated) \(\mathrm{days}\)
nbjtrav number of tillage operations \(\mathrm{ND}\)
Nminres proportion of mineral N content in organic residues (FW) \(\mathrm{\%}\)
orientrang direction of crop rows (relative to north) \(\mathrm{rad}\)
profhumrecolteuse soil depth at which moisture is considered to allow harvesting (if soil compaction is activated) \(\mathrm{cm}\)
profhumsemoir soil depth at which moisture is considered to allow sowing (if soil compaction is activated) \(\mathrm{cm}\)
profmes depth of measurement of the soil water reserve \(\mathrm{cm}\)
profres upper depth of organic residue incorporation \(\mathrm{cm}\)
profsem depth of sowing \(\mathrm{cm}\)
proftrav maximum depth affected by soil tillage \(\mathrm{cm}\)
qres mass of organic residues added to soil (fresh weight) \(\mathrm{t\ ha^{-1}}\)
Qtot_N total amount of mineral N fertilizer applications \(\mathrm{kg\ ha^{-1}}\)
ratiol water stress index below which irrigation is started in automatic mode (0 in manual mode) \(\mathrm{ND}\)
resk parameter 1/2 used to calculate profres (if code_auto_profres = 2): profres = proftrav *(1-exp(-resk.(proftrav-resz)) \(\mathrm{cm^{-1}}\)
ressuite type of crop residue: roots / whole_crop / straw+roots / stubble+roots / prunings \(\mathrm{ND}\)
restit option of restitution in case of pasture yes (1), no (2) \(\mathrm{code,\ 1\ to\ 2}\)
resz parameter 2/2 used to calculate profres (if code_auto_profres = 2): profres = proftrav *(1-exp(-resk.(proftrav-resz)) \(\mathrm{cm}\)
rugochisel roughness length of bare soil after chisel tillage (if soil compaction is activated) \(\mathrm{m}\)
rugolabour roughness length of bare soil after mouldboard ploughing (if soil compaction is activated) \(\mathrm{m}\)
stadecoupedf stage of automatic cut for forage crops \(\mathrm{ND}\)
stage_end_irrigauto phenological stage for ending automatic irrigations (plt, ger, lev, amf, lax, drp ,flo, sen, rec, mat, debdorm, findorm) \(\mathrm{ND}\)
stage_start_irrigauto phenological stage for starting automatic irrigations (plt, ger, lev, amf, lax, drp ,flo, sen, rec, mat, debdorm, findorm) \(\mathrm{ND}\)
stubblevegratio fraction of unharvested biomass stubble to vegetative biomass at harvest \(\mathrm{ND}\)
sucrerec minimal sugar concentration at harvest (/ fresh matter) \(\mathrm{g\ g^{-1}\ FW}\)
surfouvre1 relative area of the shelter opened the first day of opening \(\mathrm{ND}\)
surfouvre2 relative area of the shelter opened the second day of opening \(\mathrm{ND}\)
surfouvre3 relative area of the shelter opened the third day of opening \(\mathrm{ND}\)
tauxexportfauche fraction of cut which is exported \(\mathrm{ND}\)
tempfauche cumulative thermal time between two cuts of forage crops \(\mathrm{degree\ days}\)
transplastic transmission coefficient of the plastic shelter \(\mathrm{ND}\)
upvttapI thermal time from emergence (UPVT units) driving irrigation \(\mathrm{degree\ days}\)
upvttapN thermal time from emergence (UPVT units) driving fertilization \(\mathrm{degree\ days}\)
variete cultivar number corresponding to the cultivar name in the plant file \(\mathrm{ND}\)

3.3.2.4 Climatic data

General information

Climatic data are of two types:

  • parameters: defined in a weather station file, with the naming convention *_sta.xml,

  • daily meteorological data: file attached to a weather station in a specific location.

The Climate submenu (Local parameters) gives access to formatting a climate file or opening a weather station file.

Climate submenu

Figure 3.11: Climate submenu

Formatting a climate file

The mandatory daily weather data for the model must be written a specific file format. In order to write it correctly according to STICS format, one can use the included formatting tool Model inputs/Climate/Formatting a climate file.

Format weather file menu

Figure 3.12: Format weather file menu

Select the input file to use by clicking the Browse button.

Give a name for the files to be created in the box Change weather file name, without any extension. Specify the Number of headlines in the source file.

Indicate the columns separator in the file by clicking the appropriate radio button. Only two types of separators are possible: “white space” for fixed format files and “semicolon” for free format files.

To indicate which variables are to be extracted, simply fill in to which column number they correspond in the input file, and also indicate their unit. For example, if the year is in the second column in the original file, then put 2 in the Year field box.

Then, the variables will be transformed having the following format with a space separator and the right units:

  • column 1: name of weather file
  • column 2: year
  • column 3: month
  • column 4: day in month
  • column 5: Julian day
  • column 6: minimum temperature (degrees C)
  • column 7: maximum temperature (degrees C)
  • column 8: global radiation (MJ m-2 j-1)
  • column 9: Penman PET (mm j-1)
  • column 10: rainfall (mm j-1)
  • column 11: wind (m s-1)
  • column 12: vapour pressure (mbars)
  • column 13: CO2 content(ppm)

Some variables are mandatory: year, month, day in month, minimum temperature, maximum temperature, global radiation, Rainfall.

Penman PET is optional. If Penman PET is not extracted, the value -999.9 will be written in the output file. Then you will have to give the type of method to calculate PET in the station file (codeetp parameter).

Wind and Vapor pressure are also optional. If wind or vapour pressure is not extracted, the value -999.9 will be written in the output file. But they are mandatory if you choose the “Shuttleworth and Wallace” method or the “Penman calculate” method to calculate PET in the station file (codeetp parameter).

CO2 is also optional. If CO2 values are not extracted, then the default value of 330 ppm is written in the output file. If you want to use another value, click on the box use CO2 value and enter the value to use. Then all years will be filled with this value.

A climate file in STICS format corresponds to only one calendar year. If your input file contains several calendar years, then JavaStics will create as many output files as there are calendar years in the input file. Each of them will be suffixed with the year; *. YYYY.

If you want to extract only a part of the input file, then click on the box Partial format and give the beginning and end dates of the period to be extracted.

The Generate button will generate the output files.

The Save button will save the parameterisation of the climate file formatting for reusing it later with same kind of input files.

Weather station parameters file

To access to weather station files use Model inputs/Climate/Weather station

To create a new weather station file, select the station file you want to use as model in the drop-box list, click the New file button, enter a file name prefix, and then click OK. A new station file is created using as model the station file you selected previously.

To edit or view the station file, select the file to view, then click Open.

Station menu

Figure 3.13: Station menu

In the view window, the station parameters appear in the form of a tree structure whose branches can be expanded by clicking on the icons on the left of items.

There are two types of parameters:

  • options parameters: in this case, a drop-down list shows the different possible values that can be selected.

  • The parameters for which a value has to be given: in this case the value is entered in the box beside the parameter name. The icon on the right, when clicked opens a popup containing information on the parameter: description, type (numeric or alphanumeric), unit, boundaries values.

Station file

Figure 3.14: Station file

Table of parameters contained in the station files

Table 3.10: Table of parameters contained in the station file
Name Definition Unit
aangst coefficient of the Angstrom relationship for extraterrestrial radiation \(\mathrm{ND}\)
aclim climatic component to calculate actual soil evaporation (Brisson & Perrier, 1991) \(\mathrm{mm}\)
aks parameter of calculation of the energetic loss between the inside and the outside of a greenhouse \(\mathrm{W\ m^{-2}\ K^{-1}}\)
albveg albedo of the vegetation \(\mathrm{ND}\)
alphapt parameter of Priestley-Taylor formula \(\mathrm{ND}\)
altinversion altitude of inversion of the thermal gradient \(\mathrm{m}\)
altisimul altitude of simulated site \(\mathrm{m}\)
altistation altitude of the input metorological station \(\mathrm{m}\)
bangst coefficient of the Angstrom s relationship for extraterrestrial radiation \(\mathrm{ND}\)
bks parameter of calculation of the energetic lost between the inside and the outside of a greenhouse \(\mathrm{W\ m^{-2}\ K^{-1}}\)
cielclair fraction of sunny hours allowing the inversion of thermal gradient with altitude \(\mathrm{ND}\)
codadret option to calculate mountain climate taking into account the orientation: 1 = south, 2 = north \(\mathrm{code,\ 1\ to\ 2}\)
codaltitude option to activate the calculation of the climate in altitude: 1 = no, 2 = yes \(\mathrm{code,\ 1\ to\ 2}\)
codecaltemp option to activate the use of crop temperature for phasic development calculation: 1 = empirical relation, 2 = energy balance \(\mathrm{code,\ 1\ to\ 2}\)
codeclichange option to activate climate change: 1 = no, 2 =yes \(\mathrm{code,\ 1\ to\ 2}\)
codeetp option to calculate PET: 1 = forced Penman, 2 = calculated Penman, 3= Shuttleworth & Wallace, 4 = Priestley & Taylor \(\mathrm{code,\ 1\ to\ 4}\)
codemodlsnow option to calculate snow variables: 1 = unused, 2 = unused, 3 = Snow model 3 \(\mathrm{code,\ 1\ to\ 3}\)
codernet option to calculate net radiation: 1 = Brunt method, 2 = Cellier method \(\mathrm{code,\ 1\ to\ 2}\)
coefdevil multiplier coefficient of the outdoor radiation to calculate PET inside of a greenhouse \(\mathrm{ND}\)
coefrnet coefficient applied to the (outdoor) net radiation to calculate the net radiation under a greenhouse \(\mathrm{ND}\)
concrr concentration of mineral N (NH4+NO3-N) in the rain \(\mathrm{kg\ ha^{-1}\ mm^{-1}}\)
corecTrosee temperature to substract to Tmin to estimate dew point temperature (in case of missing air humidity data) \(\mathrm{^{\circ}C}\)
cvent parameter of the climate calculation under shelter \(\mathrm{ND}\)
DKmax difference between the maximum and the minimum melting rates for snow \(\mathrm{mm\ ^{\circ}C^{-1}\ day^{-1}}\)
E snow compaction parameter \(\mathrm{mm\ mm^{-1}\ day^{-1}}\)
gradtn thermal gradient in altitude for minimal temperatures \(\mathrm{^{\circ}C\ 100m^{-1}}\)
gradtninv thermal gradient in altitude for minimal temperatures under the inversion level \(\mathrm{^{\circ}C\ 100m^{-1}}\)
gradtx thermal gradient in altitude for maximal temperatures \(\mathrm{^{\circ}C\ 100m^{-1}}\)
Kmin minimum snow melting rate on 21 December \(\mathrm{mm\ ^{\circ}C^{-1}\ day^{-1}}\)
latitude latitude of the site \(\mathrm{degree}\)
NH3ref NH3 concentration in the atmosphere \(\mathrm{microgram\ m^{-3}}\)
ombragetx change in air temperature in the northern hillslope of mountains (activated if codadret=2) \(\mathrm{^{\circ}C}\)
patm atmospheric pressure \(\mathrm{hPa}\)
phiv0 parameter allowing the calculation of the climate under shelter \(\mathrm{ND}\)
Pns density of the new snow \(\mathrm{kg\ m^{-3}}\)
prof snow cover threshold for snow insulation \(\mathrm{cm}\)
ra aerodynamic resistance (used in volatilization module with the PET approach) \(\mathrm{s\ m^{-1}}\)
SWrf degree day temperature index for snow refreezing \(\mathrm{mm\ ^{\circ}C^{-1}\ day^{-1}}\)
tmaxseuil maximum temperature when snow cover is higher than prof \(\mathrm{^{\circ}C}\)
Tmf threshold temperature for snow melting \(\mathrm{^{\circ}C}\)
tminseuil minimum temperature when snow cover is higher than prof \(\mathrm{^{\circ}C}\)
trmax maximum air temperature (tmax) above which all precipitation is assumed to be rain \(\mathrm{^{\circ}C}\)
tsmax maximum air temperature (tmax) below which all precipitation is assumed to be snow \(\mathrm{^{\circ}C}\)
zr reference height of meteorological data measurement \(\mathrm{m}\)

3.4 Launching simulations

Several use cases are possible according to the objective of simulations and the number of USM to be selected for that. Which is the first step towards running simulations.

  • you can define a single USM with Running model/Create and run single USM or by clicking on the icon fleche

  • simulations can be launched for several independent USMs using Running model/Run independent USMs

  • simulations can be launched for a crop rotation – that means,several successive USMs that are initialised with the data from the preceding USM. Use Running model/Run successive USMs

  • one or several USMs can be launched for parameter optimization with Running model/Run parameter optimization.

3.4.1 Create and run a single USM

The USM selection dialogue box is displayed. It lets you choose among the various simulation options.

In a newly created workspace directory, an example USM has already been created (File/New workspace). It is called maize. All you need to do is to modify the parameters of the simulation.

If simulation units have already been created, in the Choose an USM drop-box list, simply select the USM name you want to use.

The choice of USM simulation options can be done either in the file selection dialogue box or by directly editing the input areas.

The options let you set the climate files, the type of plant, the crop parameters, the type of soil and the different initial states of the system; and finally the LAI file for forcing values with a daily profile instead of calculating them.

You can also create new USMs or delete USMs.

Each USM represents one of the specific simulation options you have defined. A list of these USMs and their definition is stored between each call to STICS in the file usms.xml in the work directory.

When the different simulation options have been chosen, they can be saved by clicking Save. They can also be saved in a new USM file by clicking Save as and entering a new USM name (20 characters length). A USM can also be deleted by clicking Remove.

To launch the simulation, click on the Run button.

USM menu

Figure 3.15: USM menu

Table 3.11: Table of parameters contained in the usms.xml file
Name Definition Unit
codesimul option to define the type of crop simulation: culture or 0 (LAI calculated by the model), feuille or 1 (LAI forced) \(\mathrm{code,\ 0\ to\ 1}\)
culturean number of calendar years involved in the crop cycle (1 = 1 year e.g. for spring crops, 2 = two years, e.g. for winter crops) \(\mathrm{ND}\)
datedebut starting date of simulation \(\mathrm{julian\ day}\)
datefin ending date of simulation \(\mathrm{julian\ day}\)
fclim1 name of the first climate file \(\mathrm{ND}\)
fclim2 name of the second climate file \(\mathrm{ND}\)
finit name of the initialisation file \(\mathrm{ND}\)
flai name of the LAI file \(\mathrm{ND}\)
fobs name of the observed file \(\mathrm{ND}\)
fplt name of the plant file \(\mathrm{ND}\)
fstation name of the weather station file \(\mathrm{ND}\)
ftec name of the technical file \(\mathrm{ND}\)
nbplantes number of simulated plants \(\mathrm{ND}\)
nomsol name of the soil \(\mathrm{ND}\)
usm name of the USM \(\mathrm{ND}\)

3.4.2 Run independent USMs

Independent USMs must have been already created with Running model menu/Create and run single USM. Then, using Running model/Run independent USMs, simply select those to be used from the available USM list (left pane, using either shift or Ctrl keys + click) and then click Add.

Run independent USMs

Figure 3.16: Run independent USMs

3.4.3 Run successive USMs

As for independent USMs, successive USMs must have been already created with Running model menu/Create and run single USM, being careful to set correct start and end dates. Then, using Running model/Run successive USMs, simply select those to be used from the available USM list (left pane, using either shift or Ctrl keys + click) and then click Add.

Run successive USMs

Figure 3.17: Run successive USMs

For successive simulations, the first simulation day of an USM must be consistent with the last simulation day of the previous USM (one day before).

If this condition is not satisfied, the model will stop and an error will be logged in the modhistory.sti file (workspace directory).

The link between the successive USMs is done by passing variables values stored at simulations end.

These variables are:

  • end date of the preceding simulation,

  • system state at the end of the preceding simulation:

    • water, mineral nitrogen, and soil temperature profiles

    • residues quantities and their C/N ratio

    • stocks of organic nitrogen and carbon in the different pools (residues, humus, micro-organisms)

For perennial crop successions, the state of the crop is stored and read at the next USM. Passing variables concern:

  • Non-perennial organs : lai, temporary reserves (biomass and N), structural part of leaves and stems (biomass and N)

  • Perennial organs : structural part and reserves (biomass and N),

  • Root system : root length density in the different soil layers and their corresponding biomass and N content, root front depth.

3.4.4 Run parameter optimization

optimization menu

Figure 3.18: optimization menu

This functionality lets you adjust parameters to your observed-data sets. You can choose one or several parameters, among all available ones in the input files, and optimize their values by using one or several observed variable(s), existing in the corresponding *.obs file. Basically, observation files names must be identical to USM names.

For the calculation, the method is based on a Nelder Mead simplex algorithm and using a least squares criterion.

\[f\left( x \right) = \sqrt{\frac{\sum_{1}^{n\_ usms}{\sum_{1}^{n\_ variables}{\sum_{n = 1}^{n\_ obs}\left( \frac{\left( x_{\text{observed}} - x_{\text{calculated}} \right)*n\_ obs}{\sum_{1}^{n\_ obs}x_{\text{observed}}} \right)^{2}}}}{nb\_ obs\_ tot}}\]

\(n\_ obs\) is the number of observed values for given variable and USM.

STICS gives the possibility of optimizing most of the model parameters according to observed data.

The variables are all of those available in the observation file selected.

variables choice

Figure 3.19: variables choice

The parameters are those found in the 6 types of input files: general parameters, plant parameters, crop management parameters, soil parameters, station parameters, initialisation parameters. These parameters are specified in the Optimisable parameters appendix and may use bounds specified in each of the parameter files.

The “repetitions” cell fix the number of the set of run with one starting initial value.

parameter choice

Figure 3.20: parameter choice

The user could choose these initial values or if there are less values than the repetitions the algorithm choose random values in the range specified. The initial Values fixed by the user must be separated with “/” ) In the following example

parameter choice with random initial values

Figure 3.21: parameter choice with random initial values

The outputs of the optimization are displayed on the screen and saved to the file sortieOptim.csv

optimisation results

Figure 3.22: optimisation results

Optimization stops when the spread between the criterion of each iteration has reached a minimum of 10-4 or after 1,000 iterations.

The optimisation results are described in a summary way in the repetitionSpecifics.csv file and in more detail in the file bufferOptimDetails.csv

The output variables to which these parameters are keyed are those found in the daily output files mod_s[USM].sti (USM=USM name), and in the corresponding observation files (*.obs).

Warning 1: the parameters files are not modified by the optimization! You have to change the chosen parameter values in the file parameters and run the model to see the results.

Then you can view the results of the optimization using Model outputs/Dynamic graphics by comparing the simulated data (mod_s[USM].sti file) against the observed data (.obs file).

Warning 2 : if you want optimize together in the same time parameters from 2 plant files, then the 2 plant files must be in the same directory (in the plant directory of the workspace ou in the main plant directory ) .

More complete and performing tools exist for optimizing: see part faire un lien vers la parties tools.

3.4.5 what to do when the simulation does not run

If you read the message: “The result file mod_b[USM].sti can’t be found”, this means that the simulation has failed ([USM]=USM name).

The first thing to do is to look in the history file: modhistory.sti, which is a log file giving the parameter values used and warning/error messages concerning the simulation.

This file is overwritten when launching a new simulation.

You can also post a question or look for more help on the STICS forum: https://w3.avignon.inra.fr/forge/projects/stics_main_projecu/boards

As an overall recommendation, avoid the use of spaces in directory/file names, because it could generate problems with the JavaStics interface or JavaStics command line tool.

3.5 Model outputs

This menu is used for:

  • Choosing the type of outputs you want (choice of variables, etc.): Model outputs/Choosing outputs

  • Viewing your outputs in the form of graphics, Model outputs/Dynamic graphics

3.5.1 Choosing output

This window lets you choose the type of outputs you want (choice of variables or time-step) before launching simulations.

Choosing Outputs

Figure 3.23: Choosing Outputs

3.5.1.1 Output files

Simulation outputs types are optional in STICS; one can make his own selection among these outputs files types:

  • balance files: mod_b[USM].sti which describe the different stages of the simulated crop and balances.

  • history file: modhistory.sti, which is a log file that gives you the parameter values used and warning or error messages concerning the simulation. This file is overwritten with each new simulation.

  • daily output files: mod_s[USM].sti, containing the variables chosen within the state variables simulated by the model.

  • report file (dates and/or stages): mod_rapport.sti, a file that gives a synthesis of the state variables chosen on a line corresponding to a date and/or stage. This file is written in an append mode, so it is incremented by one or several lines by each simulation.

  • profile file (dates or frequency): profil.sti, which gives you a state variable of temperature or soil humidity along the depth of the soil and for a few chosen dates. This file is overwritten by each new simulation.

The user chooses the desired output files via the flagecriture numerical parameter of the param_gen.xml file:

1 = modhistory.sti

2 = daily outputs

4 = report outputs

8 = balance outputs

16 = profile outputs

32 = debug outputs (currently not operational)

64 = screen outputs

Here are a few standard combinations of outputs files, the resulting flagecriture numerical code is the sum of the individual chosen files code.

Value of flagecriture modhistory.sti daily outputs report outputs balance outputs profile outputs debug outputs screen outputs
1 2 4 8 16 32 64
1 x
2 x
4 x
8 x
16 x
32 X (currently not operational)
64 x
128
Some examples
31(standard outputs) x x x x x
13 (synthesis outputs) x x x
95 (detailed outputs) x x x x x x
Your outputs…

3.5.1.2 Output variables

The three dialogues for choosing the output variables are as follows and correspond to the three sub-menus of the window above:

  • Configuring the daily outputs file content

The daily output files mod_s[USM].sti ([USM]= USM name) give the daily values of output variables chosen among the 600 variables calculated by the model.

These variables are described in the output variables annex.

Daily outputs variables choice

Figure 3.24: Daily outputs variables choice

The user configuration can be used in each of the output selection dialogue boxes.

It operates as follows: Each time you define a new output configuration, it is used for all the subsequent simulations until you define a new one, and is identified as a user configuration.

Each configuration is specific to the current workspace or simulation directory.

Thus you have access to two configurations – the default configuration, which corresponds to the daily output for a fixed list of variables, and the user configuration, which is the one that is saved each time you Click OK.

You can also load an already existing user configuration or the default configuration again.

  • Configuring the report file content

The file mod_rapport.sti gives the values of the variables you have selected at chosen dates and/or stages.

Three options are possible:

  • at fixed dates, in which case you need to enter these dates in the same way as in the profile dialogue box (maximum 20 dates).

  • at development stages dates you select by checking boxes.

  • Combining the two preceding options

Be aware that this file has a particular status because it is not renewed for each simulation run, so it contains the results of one or several USMs simulations until it’s deleted.

The report file mod_rapport.sti

Figure 3.25: The report file mod_rapport.sti

  • Configuring the soil profile output file

For the outputs in the profile file mod_profil.sti you may choose among five variables whose values will be given for each cm. of soil on 20 days chosen for the simulation.

You have two possible options for the dates:

  • option 1: At fixed dates, in which case you need to enter these dates (maximum 20 dates).

  • option 2: At a certain frequency starting with a given date (maximum 20 dates)

The report file mod_profil.sti

Figure 3.26: The report file mod_profil.sti

This file, mod_profil.sti, is overwritten at each simulation. If you want to keep it, you need to rename it before re-running a new simulation.

The file can be displayed in a spreadsheet or graphics program.

It is formatted as follows:

  • 1 line for the name of the variables,

  • 1 line with the chosen dates,

  • 1 line per cm of soil over 2 m depth, columns correspond to the chosen dates.

3.5.2 Dynamics graphics

This dialogue box lets you create charts (maximum 4 per page).

It can also be opened using the button.

Chart selection

Figure 3.27: Chart selection

The display looks like this:

Charts can be printed by clicking the Print… button.

JavaStics lets you display 1 to 2 daily output variables and optionally corresponding observations (from the .obs file). As many variables as desired can be displayed in a chart, keeping in mind that there is one single scale per chart.

3.6 Observations

The Observations menu is used for:

  • generating an interpolated LAI file from observed data

  • entering observed data in an [USM].obs file (create or edit mode)

Observations

Figure 3.28: Observations

3.6.1 LAI fitting

This STICS module generates a daily file of LAI values performing a an interpolation from a file of non-continuous observed values. The parameters of the fitting curve equation are to be refined for maximizing the goodness of fit.

By default, when selecting a species using the drop down list the curve parameters are fixed with default values; parameters check boxes are unchecked. When check boxes are checked, parameters values are determined automatically.

LAI interpolation

Figure 3.29: LAI interpolation

LAI s fitting

Figure 3.30: LAI s fitting

When the calculation is successful, you can call up a graphical display of the resulting interpolation by clicking the View the chart button.

The report file mod_rapport.sti

Figure 3.31: The report file mod_rapport.sti

If the calculation seems not to run correctly (the LAI curve shows nothing or shows wrong parameters), you can:

1 - look in the adjust_lai.txt file if there are information about the problem.

2 - perform the calculation once imposing the interpolation parameters (don’t check the boxes) to try to view ajustement against observed data and see if the emergence date and the basis for calculation sums of temperatures is correct.

3.6.2 Observed data

The Observations/Observed sub-menu launches a very simplified spreadsheet. It lets you enter or view observed data.

These files, with a .obs extension, are the ones used to be compared with simulations daily output variables stored for each simulation in mod_s[USM].sti files.

They may be used either when doing dynamic graphics or in parameters optimization processing.

Observations spreadsheet

Figure 3.32: Observations spreadsheet

It’s possible to add dates and/or variables from among the 600 state variables calculated by the model.

These files are formatted using a CSV format (using a semi-colon separator) and may also be generated directly in a spreadsheet. They must contain a header line containing the STICS output variables name

Notice. be careful that the jul column contains days number within a year (between 1 and 365 or 366, see tables 5.1 and 5.2), as in daily output files (mod_s*.sti)

The other first 3 columns headers correspond to year (ian), month (mo), day of month (jo) for each date.

3.7 Tools

The Select/Add Stics model version allows to choose the version of STICS used.

TODO : a revoir

By default, only the current version (STICS V10.0.0, delivered with JavaStics V1.5.0) is available under this item. Users developing their own version of the executable will be able to choose it or add a new one. That is to say that an other executable, than the given standard one, produced from STICS V10.0.0 fortran sources, without any changes in input files is possible to add and use in the JavaStics interface.

An important point is to be considered, an older version of STICS than the current V10.0.0 will not be usable with this JavaStics interface, either for editing files or running the model (i.e text files generation will fail). Changes made on input files laid to JavaStics interface modifications incompatible with older STICS versions.

For the future, we plan to keep backward compatibility as possible as we can.

Tools

Figure 3.33: Tools

4 R packages tools for Stics

4.1 Introduction

Apart from the JavaStics interface and partially relying on the JavaStics command line interface some R packages have been developed for managing Stics input and output files, and also for running the model for different use cases (simple, successive, parameter estimation, model evaluation)

They are available on github through a packages suite here: https://github.com/SticsRPacks

The installation of this package starts the installation of the several packages (last releases): * SticsRFiles * SticsOnR * CroPlotR * CroptimizR

Loading the SticsRPacks library will automatically load these packages.

add link to github resources

4.2 Managing Stics files

4.2.1 Upgrading XML files from the previous version (9.2)

The Stics files formats V10.0.0 have changed since the 9.2 version, so a conversion is needed. The SticsRFiles package provides functions for upgrading existing files contained in a 9.2 version workspace into V10.0.0 version ones. The underlying functions called for upgrading all the files may be used individually for each kind of file (i.e. USMs file, initialisation files, crop management files, etc … ).

cite functions ?

4.2.2 Getting information from inputs and outputs

parameters , output variables

4.2.3 Stics files manipulations

4.2.3.1 Extracting parameters

4.2.3.2 Replacing parameters

4.2.3.3 Generating files

  • XML from XLS or CSV files

can be used by JavaStics interfaces, or transformed in model files

  • Text from XML files

that can be read by the model)

4.2.4 Getting data from outputs or observations files

4.3 Running simulations

4.3.1 Using javastics

4.3.2 Using Stics

text files (cf gen)

wrapper

use case

4.4 Improving parameterization and evaluating Stics

4.4.1 Parameters optimization

CroptimizR package

4.4.2 Model performances evaluation

CroPlotR

5 Appendices

5.1 Dates in STICS

The dates in the STICS input files are all in Julian days (between 1 and 731) – that is, calculated from 1 January of the year of the start of the simulation.

You can calculate it quickly using the table included here:

Table 5.1: Non-Leap Year
DATE JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC
1 1 32 60 91 121 152 182 213 244 274 305 335
2 2 33 61 92 122 153 183 214 245 275 306 336
3 3 34 62 93 123 154 184 215 246 276 307 337
4 4 35 63 94 124 155 185 216 247 277 308 338
5 5 36 64 95 125 156 186 217 248 278 309 339
6 6 37 65 96 126 157 187 218 249 279 310 340
7 7 38 66 97 127 158 188 219 250 280 311 341
8 8 39 67 98 128 159 189 220 251 281 312 342
9 9 40 68 99 129 160 190 221 252 282 313 343
10 10 41 69 100 130 161 191 222 253 283 314 344
11 11 42 70 101 131 162 192 223 254 284 315 345
12 12 43 71 102 132 163 193 224 255 285 316 346
13 13 44 72 103 133 164 194 225 256 286 317 347
14 14 45 73 104 134 165 195 226 257 287 318 348
15 15 46 74 105 135 166 196 227 258 288 319 349
16 16 47 75 106 136 167 197 228 259 289 320 350
17 17 48 76 107 137 168 198 229 260 290 321 351
18 18 49 77 108 138 169 199 230 261 291 322 352
19 19 50 78 109 139 170 200 231 262 292 323 353
20 20 51 79 110 140 171 201 232 263 293 324 354
21 21 52 80 111 141 172 202 233 264 294 325 355
22 22 53 81 112 142 173 203 234 265 295 326 356
23 23 54 82 113 143 174 204 235 266 296 327 357
24 24 55 83 114 144 175 205 236 267 297 328 358
25 25 56 84 115 145 176 206 237 268 298 329 359
26 26 57 85 116 146 177 207 238 269 299 330 360
27 27 58 86 117 147 178 208 239 270 300 331 361
28 28 59 87 118 148 179 209 240 271 301 332 362
29 29 88 119 149 180 210 241 272 302 333 363
30 30 89 120 150 181 211 242 273 303 334 364
31 31 90 151 212 243 304 365
Table 5.2: Leap Year
DATE JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC
1 1 32 61 92 122 153 183 214 245 275 306 336
2 2 33 62 93 123 154 184 215 246 276 307 337
3 3 34 63 94 124 155 185 216 247 277 308 338
4 4 35 64 95 125 156 186 217 248 278 309 339
5 5 36 65 96 126 157 187 218 249 279 310 340
6 6 37 66 97 127 158 188 219 250 280 311 341
7 7 38 67 98 128 159 189 220 251 281 312 342
8 8 39 68 99 129 160 190 221 252 282 313 343
9 9 40 69 100 130 161 191 222 253 283 314 344
10 10 41 70 101 131 162 192 223 254 284 315 345
11 11 42 71 102 132 163 193 224 255 285 316 346
12 12 43 72 103 133 164 194 225 256 286 317 347
13 13 44 73 104 134 165 195 226 257 287 318 348
14 14 45 74 105 135 166 196 227 258 288 319 349
15 15 46 75 106 136 167 197 228 259 289 320 350
16 16 47 76 107 137 168 198 229 260 290 321 351
17 17 48 77 108 138 169 199 230 261 291 322 352
18 18 49 78 109 139 170 200 231 262 292 323 353
19 19 50 79 110 140 171 201 232 263 293 324 354
20 20 51 80 111 141 172 202 233 264 294 325 355
21 21 52 81 112 142 173 203 234 265 295 326 356
22 22 53 82 113 143 174 204 235 266 296 327 357
23 23 54 83 114 144 175 205 236 267 297 328 358
24 24 55 84 115 145 176 206 237 268 298 329 359
25 25 56 85 116 146 177 207 238 269 299 330 360
26 26 57 86 117 147 178 208 239 270 300 331 361
27 27 58 87 118 148 179 209 240 271 301 332 362
28 28 59 88 119 149 180 210 241 272 302 333 363
29 29 60 89 120 150 181 211 242 273 303 334 364
30 30 90 121 151 182 212 243 274 304 335 365
31 31 91 152 213 244 305 366

5.2 Model inputs

The input options and parametrisation are described in details in the OpenStics book (“Conceptual framework, equations and uses of the STICS soil-crop model”)

TODO : mettre lien vers le book!

The parametrisation options codes are described in the section “Formalisation options” attached to the chapter “Tools for smart use of the standard STICS model version”

The parametrisation is presented in the same chapter, and is organised in specific sections: one section for the plant , one for the soil, one for the crop management and one for the system initialisations.

5.3 Model outputs

Table 5.3: State variables calculated by the model
Name Definition Unit
abso(n) N uptake rate by the crop \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
age_prairie age of the forage crop since sowing \(\mathrm{year}\)
airg(n) daily amount of irrigation water \(\mathrm{mm\ day^{-1}}\)
albedolai albedo of the crop including soil and vegetation \(\mathrm{ND}\)
allocfruit allocation ratio of assimilates to the fruits \(\mathrm{0\ to\ 1}\)
amm_1_30 amount of NH4-N in the soil layer 1 to 30 cm \(\mathrm{kg\ ha^{-1}}\)
amm_31_60 amount of NH4-N in the soil layer 31-60 cm \(\mathrm{kg\ ha^{-1}}\)
amm_61_90 amount of NH4-N in the soil layer 61-90 cm \(\mathrm{kg\ ha^{-1}}\)
ammomes amount of NH4-N in soil over the depth profmes \(\mathrm{kg\ ha^{-1}}\)
amptcultmat mean daily temperature range (tcult) during the reproductive phase (stages lax - rec) \(\mathrm{^{\circ}C}\)
anit(n) daily amount of fertiliser-N added to crop \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
anit_engrais(n) Daily nitrogen provided by fertiliser \(\mathrm{kgN\ ha^{-1}\ j^{-1}}\)
anit_uree(n) amount of animal urine returned to the soil \(\mathrm{kgN\ ha^{-1}\ j^{-1}}\)
anoxmoy index of anoxia over the root depth \(\mathrm{0\ to\ 1}\)
AZamm(1) amount of NH4-N in soil layer 1 \(\mathrm{kg\ ha^{-1}}\)
AZamm(2) amount of NH4-N in soil layer 2 \(\mathrm{kg\ ha^{-1}}\)
AZamm(3) amount of NH4-N in soil layer 3 \(\mathrm{kg\ ha^{-1}}\)
AZamm(4) amount of NH4-N in soil layer 4 \(\mathrm{kg\ ha^{-1}}\)
AZamm(5) amount of NH4-N in soil layer 5 \(\mathrm{kg\ ha^{-1}}\)
azlesd daily amount of NO3-N leached in mole drains \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
AZnit(1) amount of NO3-N in soil layer 1 \(\mathrm{kg\ ha^{-1}}\)
AZnit(2) amount of NO3-N in soil layer 2 \(\mathrm{kg\ ha^{-1}}\)
AZnit(3) amount of NO3-N in soil layer 3 \(\mathrm{kg\ ha^{-1}}\)
AZnit(4) amount of NO3-N in soil layer 4 \(\mathrm{kg\ ha^{-1}}\)
AZnit(5) amount of NO3-N in soil layer 5 \(\mathrm{kg\ ha^{-1}}\)
azomes amount of NO3-N in soil over the depth profmes \(\mathrm{kg\ ha^{-1}}\)
azsup_by_horizon(1) lixiviation under the horizon 1 \(\mathrm{kgN\ ha^{-1}}\)
azsup_by_horizon(2) lixiviation under the horizon 2 \(\mathrm{kgN\ ha^{-1}}\)
azsup_by_horizon(3) lixiviation under the horizon 3 \(\mathrm{kgN\ ha^{-1}}\)
azsup_by_horizon(4) lixiviation under the horizon 4 \(\mathrm{kgN\ ha^{-1}}\)
azsup_by_horizon(5) lixiviation under the horizon 5 \(\mathrm{kgN\ ha^{-1}}\)
azsup_under_profmes lixiviation under the depth of measurement profmes \(\mathrm{kgN\ ha^{-1}}\)
bouchon index showing if the shrinkage slots are opened (0) or closed (1) \(\mathrm{0/^{1}}\)
Cb amount of C in the microbial biomass decomposing organic residues mixed with soil \(\mathrm{kg\ ha^{-1}}\)
Cbmulch amount of C in the microbial biomass decomposing organic residues at soil surface (mulch) \(\mathrm{kg\ ha^{-1}}\)
cdemande cumulative amount of N needed by the plant (plant needs) \(\mathrm{kg\ ha^{-1}}\)
cEdirect total evaporation (water evaporated by the soil + intercepted by leaves and mulch) integrated over the cropping season \(\mathrm{mm}\)
cEdirecttout total evaporation (water evaporated by the soil + intercepted by leaves and mulch) integrated over the simulation period \(\mathrm{mm}\)
cep cumulative transpiration over the cropping season of plant 1 \(\mathrm{mm}\)
cep2 cumulative transpiration over the cropping season of plants 1 and 2 \(\mathrm{mm}\)
ces cumulative evaporation over the cropping season \(\mathrm{mm}\)
cestout cumulative evaporation over the simulation period \(\mathrm{mm}\)
cet cumulative evapotranspiration over the cropping season \(\mathrm{mm}\)
cet_from_lev cumulative evapotranspiration over the cropping season (from emergence or budbreak) \(\mathrm{mm}\)
cet_from_plt cumulative evapotranspiration over the cropping season (from planting or budbreak) \(\mathrm{mm}\)
cetm cumulative maximum evapotranspiration over the cropping season \(\mathrm{mm}\)
Cetmtout cumulative maximum evapotranspiration over the simulation period \(\mathrm{mm}\)
cetp cumulative potential evapotranspiration (PET) over the cropping season \(\mathrm{mm}\)
chargefruit number of filling grains or ripe fruits \(\mathrm{m^{-2}}\)
Chuma amount of active C in humified organic matter \(\mathrm{kg\ ha^{-1}}\)
Chumi amount of inert C in humified organic matter \(\mathrm{kg\ ha^{-1}}\)
Chumt amount of C in humified organic matter (active + inert fractions) \(\mathrm{kg\ ha^{-1}}\)
cintermulch cumulative amount of rain intercepted by the mulch \(\mathrm{mm}\)
cinterpluie cumulative amount of rain intercepted by the leaves \(\mathrm{mm}\)
Cmulch amount of C in the whole plant mulch \(\mathrm{kg\ ha^{-1}}\)
Cmulchdec amount of C in the decomposable mulch \(\mathrm{kg\ ha^{-1}}\)
Cmulchnd amount of C in the non decomposable mulch \(\mathrm{kg\ ha^{-1}}\)
CNgrain N concentration in fruits \(\mathrm{\%\ dry\ weight}\)
Cnondec(1) amount of C in the undecomposable mulch made of residues of type 1 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(10) amount of C in the undecomposable mulch made of residues of type 10 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(2) amount of C in the undecomposable mulch made of residues of type 2 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(3) amount of C in the undecomposable mulch made of residues of type 3 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(4) amount of C in the undecomposable mulch made of residues of type 4 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(5) amount of C in the undecomposable mulch made of residues of type 5 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(6) amount of C in the undecomposable mulch made of residues of type 6 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(7) amount of C in the undecomposable mulch made of residues of type 7 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(8) amount of C in the undecomposable mulch made of residues of type 8 \(\mathrm{kg\ ha^{-1}}\)
Cnondec(9) amount of C in the undecomposable mulch made of residues of type 9 \(\mathrm{kg\ ha^{-1}}\)
CNplante N concentration in the aboveground plant \(\mathrm{\%\ dry\ weight}\)
CO2(n) atmospheric CO2 concentration above 330 ppm \(\mathrm{ppm}\)
CO2hum daily amount of CO2-C emitted due to the mineralisation of soil humus \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
CO2res daily amount of CO2-C emitted due to the mineralisation of organic residues \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
CO2sol daily amount of CO2-C emitted due to soil mineralisation (humus and organic residues) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
codebbch_output code of the bbch stage (see plant file) \(\mathrm{0\ to\ 99}\)
concN_W_drained \(\mathrm{}\)
concNO3les nitrate concentration in drained water \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
concNO3sol(1) nitrate concentration in soil layer 1 \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
concNO3sol(2) nitrate concentration in soil layer 2 \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
concNO3sol(3) nitrate concentration in soil layer 3 \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
concNO3sol(4) nitrate concentration in soil layer 4 \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
concNO3sol(5) nitrate concentration in soil layer 5 \(\mathrm{mg\ NO^{3}\ l^{-1}}\)
condenit ratio of actual to potential denitrifying rate \(\mathrm{0\ to\ 1}\)
couvermulch cover ratio of mulch \(\mathrm{0\ to\ 1}\)
cpluie cumulative amount of rain over the simulation period \(\mathrm{mm}\)
cprecip cumulative water supply over the cropping season (precipitation + irrigation) \(\mathrm{mm}\)
cpreciptout cumulative water supply over the simulation period (precipitation + irrigation) \(\mathrm{mm}\)
Cr amount of C in organic residues mixed with soil in the profhum layer \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(1) amount of C in residues over the soil depth profhum in the residue type 1 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(10) amount of C in residues over the soil depth profhum in the residue type 10 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(2) amount of C in residues over the soil depth profhum in the residue type 2 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(3) amount of C in residues over the soil depth profhum in the residue type 3 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(4) amount of C in residues over the soil depth profhum in the residue type 4 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(5) amount of C in residues over the soil depth profhum in the residue type 5 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(6) amount of C in residues over the soil depth profhum in the residue type 6 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(7) amount of C in residues over the soil depth profhum in the residue type 7 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(8) amount of C in residues over the soil depth profhum in the residue type 8 \(\mathrm{kg\ ha^{-1}}\)
Cresiduprofil(9) amount of C in residues over the soil depth profhum in the residue type 9 \(\mathrm{kg\ ha^{-1}}\)
crg cumulative global radiation over the cropping season \(\mathrm{MJ\ m^{-2}}\)
crgtout cumulative global radiation over the simulation period \(\mathrm{MJ\ m^{-2}}\)
Crprof amount of C in deep organic residues mixed with soil (below the profhum depth) \(\mathrm{kg\ ha^{-1}}\)
Crtout total amount of C in organic residues present over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
CsurNrac C/N ratio of living roots \(\mathrm{g\ g^{-1}}\)
CsurNracmort C/N ratio of dead roots (cumulative) \(\mathrm{g\ g^{-1}}\)
CsurNres_pature C/N ratio of residues in case of pasture \(\mathrm{g\ g^{-1}}\)
CsurNsol C/N ratio of soil organic matter in the profhum layer \(\mathrm{g\ g^{-1}}\)
ctairtout cumulative air temperature (tair) over the simulation period \(\mathrm{^{\circ}C}\)
ctcult cumulative crop temperature (tcult) over the cropping season \(\mathrm{^{\circ}C}\)
ctculttout cumulative crop temperature (tcult) over the simulation period \(\mathrm{^{\circ}C}\)
ctetptout cumulative potential evapotranspiration (pet) over the simulation period \(\mathrm{mm}\)
ctmoy cumulative air temperature over the cropping season \(\mathrm{^{\circ}C}\)
cum_et0 cumulative maximum evapotranspiration over the cropping season (eop+eos) \(\mathrm{mm}\)
cum_et0_from_lev cumulative maximum evapotranspiration over the cropping season from germination or budbreak (eop+eos) \(\mathrm{mm}\)
cum_immob cumulative amount of N immobilised by the microbial biomass decomposing residues \(\mathrm{kg\ ha^{-1}}\)
cum_immob_positif cumulative amount of N immobilised by the microbial biomass decomposing residues (positive value) \(\mathrm{kg\ ha^{-1}}\)
cumlracz cumulative length of active roots per soil surface \(\mathrm{cm\ cm^{-2}}\)
cumraint cumulative intercepted radiation \(\mathrm{MJ\ m^{-2}}\)
cumrg cumulative global radiation during the stage sowing-harvest \(\mathrm{Mj\ m^{-2}}\)
cumvminh daily amount of N mineralised from humus \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
cumvminr daily amount of N mineralised from organic residues \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
da(1) bulk density of the layer 1 (recalculated by the model if codeDSTtass is 1) \(\mathrm{g\ cm^{-3}}\)
da(2) bulk density of the layer 2 (recalculated by the model if codeDSTtass is 1) \(\mathrm{g\ cm^{-3}}\)
date_irrigations(1) date of irrigation \(\mathrm{ND}\)
date_irrigations(10) date of irrigation \(\mathrm{ND}\)
date_irrigations(11) date of irrigation \(\mathrm{ND}\)
date_irrigations(12) date of irrigation \(\mathrm{ND}\)
date_irrigations(13) date of irrigation \(\mathrm{ND}\)
date_irrigations(14) date of irrigation \(\mathrm{ND}\)
date_irrigations(15) date of irrigation \(\mathrm{ND}\)
date_irrigations(16) date of irrigation \(\mathrm{ND}\)
date_irrigations(17) date of irrigation \(\mathrm{ND}\)
date_irrigations(18) date of irrigation \(\mathrm{ND}\)
date_irrigations(19) date of irrigation \(\mathrm{ND}\)
date_irrigations(2) date of irrigation \(\mathrm{ND}\)
date_irrigations(20) date of irrigation \(\mathrm{ND}\)
date_irrigations(21) date of irrigation \(\mathrm{ND}\)
date_irrigations(22) date of irrigation \(\mathrm{ND}\)
date_irrigations(23) date of irrigation \(\mathrm{ND}\)
date_irrigations(24) date of irrigation \(\mathrm{ND}\)
date_irrigations(25) date of irrigation \(\mathrm{ND}\)
date_irrigations(26) date of irrigation \(\mathrm{ND}\)
date_irrigations(27) date of irrigation \(\mathrm{ND}\)
date_irrigations(28) date of irrigation \(\mathrm{ND}\)
date_irrigations(29) date of irrigation \(\mathrm{ND}\)
date_irrigations(3) date of irrigation \(\mathrm{ND}\)
date_irrigations(30) date of irrigation \(\mathrm{ND}\)
date_irrigations(4) date of irrigation \(\mathrm{ND}\)
date_irrigations(5) date of irrigation \(\mathrm{ND}\)
date_irrigations(6) date of irrigation \(\mathrm{ND}\)
date_irrigations(7) date of irrigation \(\mathrm{ND}\)
date_irrigations(8) date of irrigation \(\mathrm{ND}\)
date_irrigations(9) date of irrigation \(\mathrm{ND}\)
day_after_begin_simul number of days from the beginning of simulation \(\mathrm{days}\)
day_after_emergence number of days after emergence \(\mathrm{days}\)
day_after_sowing days after sowing or planting \(\mathrm{day}\)
day_cut cut day \(\mathrm{julian\ day}\)
DCbmulch \(\mathrm{}\)
DChumt change in humified organic C in soil between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DCmulch change in mulch C between the beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DCr change in C of organic residues between begining and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DCrprof change in deep root C between the beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
deltai(n) daily increase in green leaf index per soil surface \(\mathrm{m^{2}\ m^{-2}\ day^{-1}}\)
deltaz rate of deepening of the root front \(\mathrm{cm\ day^{-1}}\)
demande daily N requirement of the plant to maximise crop growth \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
demandeper daily N requirement of the perennial organs to maximise crop growth \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
demanderac daily N requirementof the roots to maximise crop growth \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
demandetot daily N requirement of the plant to maximise crop growth after susbtracting N fixation \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
densite actual sowing density \(\mathrm{plants\ m^{-2}}\)
densiteequiv equivalent plant density for the understorey crop \(\mathrm{plants\ m^{-2}}\)
dfol within the shape leaf density \(\mathrm{m^{2}\ m^{-3}}\)
diftemp1intercoupe mean difference between crop and air temperatures during the vegetative phase (emergence - maximum LAI) \(\mathrm{^{\circ}C}\)
diftemp2intercoupe mean difference between crop and air temperatures during the reproductive phase (maximum LAI - maturity) \(\mathrm{^{\circ}C}\)
dltags daily growth rate of the plantlets \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
dltaisen daily change in the senescent leaf area index \(\mathrm{m^{2}\ m^{-2}\ day^{-1}}\)
dltams(n) daily growth rate of the plant \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
dltamsen daily senescence rate of the plant \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
dltaremobil daily amount of perennial reserves remobilised \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
dltaremobilN daily amount of perennial N reserves remobilised \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
dltmsrac_plante pour sorties ArchiSTICS: biomasse journaliere allouee aux racines \(\mathrm{g\ m^{2}\ sol}\)
DNbmulch change in biomass N associated with the mulch between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DNhumt change in humified organic N in soil between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DNmulch change in mulch N between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DNr change in N of organic residues between begining and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DNrprof change in N of deep dead roots between begining and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DQNtot2 change in N content of the two plants (aerial + root + perennial organs) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
drain daily amount of water drained at the base of the soil profile \(\mathrm{mm\ day^{-1}}\)
drain_from_lev cumulative amount of water drained at the base of the soil profile during the crop cycle (emergence or budbreak to harvest) \(\mathrm{mm}\)
drain_from_plt cumulative amount of water drained at the base of the soil profile during the crop cycle (planting to harvest) \(\mathrm{mm}\)
drat cumulative amount of water drained at the base of the soil profile during the simulation period \(\mathrm{mm}\)
drlsenmortalle root biomass corresponding to dead tillers \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
DSMN change in soil mineral N between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DSOC change in soil organic C (without residues) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DSOCtot change in total soil organic C (with residues) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DSON change in soil organic N (without residues) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DSONtot change in total soil organic N (with residues) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
DSTN change in total soil N (mineral + organic) between beginning and end of simulation \(\mathrm{kg\ ha^{-1}}\)
dtj(n) thermal time for root growth \(\mathrm{^{\circ}C\ d}\)
dureehumec number of hours which are wet (rainy days or days when tcult < dew point) \(\mathrm{hour}\)
dureeRH number of night hours during which relative humidity exceeds a 90% threshold \(\mathrm{hour}\)
durvie(n) actual life span of the leaf surface \(\mathrm{^{\circ}C}\)
eai equilvalent leaf area for ear \(\mathrm{m^{2}\ m^{-2}}\)
ebmax maximum value of radiation use efficiency \(\mathrm{cg\ MJ^{-1}}\)
ebmax_gr Maximum radiation use efficiency during the vegetative stage (AMF-DRP) \(\mathrm{g\ MJ^{-1}}\)
Edirect daily amount of water evaporated by the soil + intercepted by leaves and mulch \(\mathrm{mm\ day^{-1}}\)
efda reduction factor on root growth due to physical constraint (through bulk density) \(\mathrm{0\ to\ 1}\)
efdensite density factor on leaf area growth \(\mathrm{0\ to\ 1}\)
efdensite_rac density factor on root growth \(\mathrm{0\ to\ 1}\)
efNrac_mean reduction factor on root growth rate due to mineral N concentration \(\mathrm{0\ to\ 1}\)
em_N2O daily amount of N2O-N emitted from soil \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
em_N2Oden daily amount of N2O-N emitted from soil by denitrification \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
em_N2Onit daily amount of N2O-N emitted from soil by nitrification \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
Emd daily amount of water directly evaporated after leaves interception \(\mathrm{mm\ day^{-1}}\)
emulch daily amount of water directly evaporated after mulch interception \(\mathrm{mm\ day^{-1}}\)
eo intermediary variable for the computation of evapotranspiration \(\mathrm{mm\ day^{-1}}\)
eop daily maximum transpiration flux \(\mathrm{mm\ day^{-1}}\)
eos daily maximum evaporation flux \(\mathrm{mm\ day^{-1}}\)
ep daily actual transpiration flux \(\mathrm{mm\ day^{-1}}\)
epc_recal(1) thickness of the soil layer 1 (recalculated by the model if codeDSTtass is 1) \(\mathrm{cm}\)
epc_recal(2) thickness of the soil layer 2 (recalculated by the model if codeDSTtass is 1) \(\mathrm{cm}\)
epc_recal(3) thickness of the soil layer 3 (recalculated by the model if codeDSTtass is 1) \(\mathrm{cm}\)
epc_recal(4) thickness of the soil layer 4 (recalculated by the model if codeDSTtass is 1) \(\mathrm{cm}\)
epc_recal(5) thickness of the soil layer 5 (recalculated by the model if codeDSTtass is 1) \(\mathrm{cm}\)
epsib radiation use efficiency \(\mathrm{t\ ha^{-1}\ MJ^{-1}\ m^{2}}\)
esol daily actual soil evaporation flux \(\mathrm{mm\ day^{-1}}\)
et daily evapotranspiration (esol + ep) \(\mathrm{mm\ day^{-1}}\)
et0 daily maximun evapotranspiration flux (transpiration + soil evaporation) \(\mathrm{mm}\)
etm daily maximum evapotranspiration (esol + eop) \(\mathrm{mm\ day^{-1}}\)
etm_etr1moy etm/etr ratio on the vegetative phase \(\mathrm{0\ to\ 1}\)
etm_etr2moy etm/etr ratio on the reproductive phase \(\mathrm{0\ to\ 1}\)
etpp(n) daily potential evapotranspiration as given by the formula of Penman \(\mathrm{mm\ day^{-1}}\)
etr_etm1moy etr/etm ratio on the vegetative phase \(\mathrm{0\ to\ 1}\)
etr_etm2moy etr/etm ratio on the reproductive phase \(\mathrm{0\ to\ 1}\)
exces(1) amount of water in the macroporosity of the layer 1 \(\mathrm{mm}\)
exces(2) amount of water in the macroporosity of the layer 2 \(\mathrm{mm}\)
exces(3) amount of water in the macroporosity of the layer 3 \(\mathrm{mm}\)
exces(4) amount of water in the macroporosity of the layer 4 \(\mathrm{mm}\)
exces(5) amount of water in the macroporosity of the layer 5 \(\mathrm{mm}\)
exobiom reduction factor on biomass growth due to water excess \(\mathrm{0\ to\ 1}\)
exofac waterlogging index \(\mathrm{0\ to\ 1}\)
exofac1moy mean value of the waterlogging index during the vegetative stage (emergence - fruit establishment) \(\mathrm{0\ to\ 1}\)
exofac2moy mean value of the waterlogging index during the reproductive stage (fruit establishment - maturity) \(\mathrm{0\ to\ 1}\)
exolai reduction factor on leaf growth due to water excess \(\mathrm{0\ to\ 1}\)
fapar proportion of the radiation intercepted \(\mathrm{0\ to\ 1}\)
fco2 specie-dependant CO2 effect on radiation use efficiency \(\mathrm{ND}\)
fco2s specie-dependant CO2 effect onstomate closure \(\mathrm{ND}\)
fgelflo reduction factor on the number of fruits due to frost \(\mathrm{0\ to\ 1}\)
fixmaxvar maximal rate of BNF (symbiotic fixation) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
fixpot potential rate of BNF (symbiotic fixation) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
fixreel actual rate of BNF (symbiotic fixation) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
flurac daily amount of N taken up by the plant when N uptake is limited by the plant capacity absorption \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
flusol daily amount of N taken up by the plant when N uptake is limited by the transfer from soil to root \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
fpari radiation effect on conversion efficiency \(\mathrm{g\ MJ^{-1}}\)
fpari_gr radiation factor on the calculation of conversion efficiency \(\mathrm{g\ MJ^{-1}}\)
fpft daily sink capacity of fruits \(\mathrm{g\ m^{-2}\ day^{-1}}\)
fpv(n) daily sink capacity of growing leaves \(\mathrm{g\ m^{-2}\ day^{-1}}\)
FsNH3 daily amount of NH3-N emitted from soil by volatilisation \(\mathrm{micro\ g\ m^{-2}\ day^{-1}}\)
fstressgel reduction factor on leaf growth due to frost \(\mathrm{0\ to\ 1}\)
ftemp reduction factor on biomass growth due to temperature-related epsibmax \(\mathrm{0\ to\ 1}\)
fxa reduction factor on BNF (symbiotic fixation) due to soil anoxia \(\mathrm{0\ to\ 1}\)
fxn reduction factor on BNF (symbiotic fixation) due to mineral N concentration \(\mathrm{0\ to\ 1}\)
fxt reduction factor on BNF (symbiotic fixation) due to soil temperature \(\mathrm{0\ to\ 1}\)
fxw reduction factor on BNF (symbiotic fixation) due to soil water content \(\mathrm{0\ to\ 1}\)
gel1 stress factor on leaves damaged by frost before amf stage (end of juvenile phase ) \(\mathrm{0\ to\ 1}\)
gel1_percent proportion of leaves damaged by frost before amf stage (end of juvenile phase ) \(\mathrm{\%}\)
gel2 stress factor on leaves damaged by frost after amf stage (end of juvenile phase ) \(\mathrm{0\ to\ 1}\)
gel2_percent proportion of leaves damaged by frost after amf stage (end of juvenile phase ) \(\mathrm{\%}\)
gel3 stress factor on flowers or fruits damaged by frost \(\mathrm{0\ to\ 1}\)
gel3_percent proportion of flowers or fruits damaged by frost \(\mathrm{\%}\)
GHG Greenhouse Gas emission (CO2 + N2O) expressed in CO2eq/ha =Qem_N2O44/28296 -DSOC*44/12 \(\mathrm{kg\ ha^{-1}}\)
grain_dry_weight_mg Grain unit dry weight \(\mathrm{mg}\)
H2Orec water content of harvested organs \(\mathrm{0\ to\ 1}\)
H2Orec_percent water content of harvested organs \(\mathrm{\%\ fresh\ weight}\)
hauteur height of canopy \(\mathrm{m}\)
HI_C harvest index for carbon \(\mathrm{0\ to\ 1}\)
HI_N harvest index for nitrogen \(\mathrm{0\ to\ 1}\)
Hmax maximum height of water table between drains \(\mathrm{cm}\)
Hnappe height of water table affecting plant growth \(\mathrm{cm}\)
Hpb minimum depth of perched water table \(\mathrm{cm}\)
Hph maximum depth of perched water table \(\mathrm{cm}\)
HR(1) water content of the soil layer 1 \(\mathrm{\%\ dry\ weight}\)
HR(2) water content of the soil layer 2 \(\mathrm{\%\ dry\ weight}\)
HR(3) water content of the soil layer 3 \(\mathrm{\%\ dry\ weight}\)
HR(4) water content of the soil layer 4 \(\mathrm{\%\ dry\ weight}\)
HR(5) water content of the soil layer 5 \(\mathrm{\%\ dry\ weight}\)
HR_mm(1) water content of the soil layer 1 \(\mathrm{mm}\)
HR_mm(2) water content of the soil layer 2 \(\mathrm{mm}\)
HR_mm(3) water content of the soil layer 3 \(\mathrm{mm}\)
HR_mm(4) water content of the soil layer 4 \(\mathrm{mm}\)
HR_mm(5) water content of the soil layer 5 \(\mathrm{mm}\)
HR_mm_1_30 water content of the layer 1-30 cm \(\mathrm{mm}\)
HR_mm_31_60 water content of the layer 31-60 cm \(\mathrm{mm}\)
HR_mm_61_90 water content of the layer 61-90 cm \(\mathrm{mm}\)
HR_vol_1_10 water content of the layer 1-10 cm \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_1_30 water content of the layer 1-30 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_121_150 water content of the layer 121-150 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_151_180 water content of the layer 151-180 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_31_60 water content of the layer 31-60 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_61_90 water content of the layer 61-90 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
HR_vol_91_120 water content of the layer 91-120 cm (table) \(\mathrm{mm^{-3}\ mm^{-3}}\)
huile oil content of harvested organs \(\mathrm{0\ to\ 1}\)
huile_percent oil content of harvested organs \(\mathrm{\%\ fresh\ weight}\)
humair air moisture content \(\mathrm{0\ to\ 1}\)
humair_percent air moisture content \(\mathrm{\%\ saturation}\)
humidite air moisture content in the canopy \(\mathrm{0\ to\ 1}\)
humidite_percent air moisture content in the canopy \(\mathrm{\%\ saturation}\)
humirac_mean reduction factor on root growth due to soil water content (mean value over the root profile) \(\mathrm{0\ to\ 1}\)
hur_10_vol soil water content in the soil at 10 cm \(\mathrm{cm/cm}\)
husup_by_horizon(1) drainage under the horizon 1 \(\mathrm{mm}\)
husup_by_horizon(2) drainage under the horizon 2 \(\mathrm{mm}\)
husup_by_horizon(3) drainage under the horizon 3 \(\mathrm{mm}\)
husup_by_horizon(4) drainage under the horizon 4 \(\mathrm{mm}\)
husup_by_horizon(5) drainage under the horizon 5 \(\mathrm{mm}\)
husup_under_profmes drainage under the depth of measurement profmes \(\mathrm{mm}\)
iamfs date of amf stage (maximum acceleration of leaf growth, end of juvenile phase ) \(\mathrm{julian\ day}\)
idebdess date of onset of water dynamics in harvested organs \(\mathrm{julian\ day}\)
idebdorms date of entry into dormancy \(\mathrm{julian\ day}\)
idrps starting date of filling of harvested organs \(\mathrm{julian\ day}\)
ifindorms date of emergence from dormancy \(\mathrm{julian\ day}\)
iflos date of flowering \(\mathrm{julian\ day}\)
iflos_minus_150 date of flowering minus150 degrees day \(\mathrm{julian\ day}\)
iflos_plus_150 date of flowering plus 150 degrees day \(\mathrm{julian\ day}\)
igers date of germination \(\mathrm{julian\ day}\)
ilans date of lan stage (leaf index nil) \(\mathrm{julian\ day}\)
ilaxs date of lax stage (leaf index maximum) \(\mathrm{julian\ day}\)
ilevs date of emergence \(\mathrm{julian\ day}\)
imats date of start of physiological maturity \(\mathrm{julian\ day}\)
imontaisons date of start of stem elongation \(\mathrm{julian\ day}\)
infil_recal(1) infiltrability parameter at the base of the layer 1 \(\mathrm{mm\ day^{-1}}\)
infil_recal(2) infiltrability parameter at the base of the layer 2 \(\mathrm{mm\ day^{-1}}\)
infil_recal(3) infiltrability parameter at the base of the layer 3 \(\mathrm{mm\ day^{-1}}\)
infil_recal(4) infiltrability parameter at the base of the layer 4 \(\mathrm{mm\ day^{-1}}\)
infil_recal(5) infiltrability parameter at the base of the layer 5 \(\mathrm{mm\ day^{-1}}\)
inn nitrogen nutrition index (NNI) \(\mathrm{0\ to\ 2}\)
inn1intercoupe average NNI during the cut (cut crop vegetative phase: emergence to maximum LAI) \(\mathrm{0\ to\ 2}\)
inn1moy average NNI during the vegetative stage \(\mathrm{0\ to\ 2}\)
inn2intercoupe average NNI during the cut (cut crop reproductive phase: maximum LAI to maturity) \(\mathrm{0\ to\ 2}\)
inn2moy average NNI during the reproductive stage \(\mathrm{0\ to\ 2}\)
innlai reduction factor on leaf growth due to NNI (nitrogen deficiency) \(\mathrm{innmin\ to\ 1}\)
inns reduction factor on biomass growth due to NNI (nitrogen deficiency) \(\mathrm{innmin\ to\ 1}\)
innsenes nitrogen stress index affecting leaves death \(\mathrm{innmin\ to\ 1}\)
inous ending date for setting of harvested organs \(\mathrm{julian\ day}\)
intermulch daily amount of water intercepted by the mulch (vegetal) \(\mathrm{mm\ day^{-1}}\)
interpluie daily amount of water intercepted by leaves \(\mathrm{mm\ day^{-1}}\)
iplts date of sowing or planting \(\mathrm{julian\ day}\)
irazo(n) nitrogen harvest index \(\mathrm{0\ to\ 1}\)
ircarb(n) carbon harvest index \(\mathrm{0\ to\ 1}\)
irecs date of harvest (first if several) \(\mathrm{julian\ day}\)
irrigjN daily amount of mineral N added by irrigation \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
irrigN cumulative amount of mineral N added by irrigation \(\mathrm{kg\ ha^{-1}}\)
isens date of begninning leaf senescence stage \(\mathrm{julian\ day}\)
izrac water excess stress index on roots \(\mathrm{0\ to\ 1}\)
lai(n) leaf area index (table) \(\mathrm{m^{2}\ m^{-2}}\)
lai_mx_av_cut LAI before cut (for cut crops , for others = lai(n) ) \(\mathrm{ND}\)
laimax maximum leaf area index \(\mathrm{m^{2}\ m^{-2}}\)
laisen(n) leaf area index of senescent leaves (table) \(\mathrm{m^{2}\ m^{-2}}\)
largeur width of the plant shape \(\mathrm{m}\)
leaching_from_lev cumulative amount of NO3-N leached at the base of the soil profile during the crop cycle ( emergence or budbreak to harvest) \(\mathrm{kg\ ha^{-1}}\)
leaching_from_plt cumulative amount of NO3-N leached at the base of the soil profile during the crop cycle (planting to harvest) \(\mathrm{kg\ ha^{-1}}\)
leai Leaf+ear area index = lai +eai \(\mathrm{m^{2}\ m^{-2}}\)
lessiv daily amount of NO3-N leached at the base of the soil profile \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
lracf(1) root length density of fine roots in layer 1 \(\mathrm{cm\ cm^{-3}}\)
lracf(2) root length density of fine roots in layer 2 \(\mathrm{cm\ cm^{-3}}\)
lracf(3) root length density of fine roots in layer 3 \(\mathrm{cm\ cm^{-3}}\)
lracf(4) root length density of fine roots in layer 4 \(\mathrm{cm\ cm^{-3}}\)
lracf(5) root length density of fine roots in layer 5 \(\mathrm{cm\ cm^{-3}}\)
lracg(1) root length density of coarse roots in layer 1 \(\mathrm{cm\ cm^{-3}}\)
lracg(2) root length density of coarse roots in layer 2 \(\mathrm{cm\ cm^{-3}}\)
lracg(3) root length density of coarse roots in layer 3 \(\mathrm{cm\ cm^{-3}}\)
lracg(4) root length density of coarse roots in layer 4 \(\mathrm{cm\ cm^{-3}}\)
lracg(5) root length density of coarse roots in layer 5 \(\mathrm{cm\ cm^{-3}}\)
LRACH(1) root length density in soil layer 1 \(\mathrm{cm\ cm^{-3}}\)
LRACH(2) root length density in soil layer 2 \(\mathrm{cm\ cm^{-3}}\)
LRACH(3) root length density in soil layer 3 \(\mathrm{cm\ cm^{-3}}\)
LRACH(4) root length density in soil layer 4 \(\mathrm{cm\ cm^{-3}}\)
LRACH(5) root length density in soil layer 5 \(\mathrm{cm\ cm^{-3}}\)
lracsentotf cumulative length of senescent roots \(\mathrm{cm\ root\ cm\ -2\ soil}\)
lracsentotg cumulative length of senescent roots \(\mathrm{cm\ root\ cm\ -2\ soil}\)
mabois biomass removed by pruning \(\mathrm{t\ ha^{-1}}\)
maenfruit biomass of harvested organ envelops \(\mathrm{t\ ha^{-1}}\)
mafauche biomass of forage cuts \(\mathrm{t\ ha^{-1}}\)
mafauchetot cumulative biomass of forage cuts \(\mathrm{t\ ha^{-1}}\)
mafeuil biomass of leaves \(\mathrm{t\ ha^{-1}}\)
mafeuil_kg_ha Dry matter of leaves \(\mathrm{kg\ ha^{-1}}\)
mafeuiljaune biomass of yellow leaves \(\mathrm{t\ ha^{-1}}\)
mafeuiltombe biomass of fallen leaves \(\mathrm{t\ ha^{-1}}\)
mafeuiltombefauche biomass of fallen leaves between two cuts \(\mathrm{t\ ha^{-1}}\)
mafeuilverte biomass of green leaves \(\mathrm{t\ ha^{-1}}\)
mafou biomass of harvested organs for cut crops \(\mathrm{t\ ha^{-1}}\)
mafrais aboveground fresh matter \(\mathrm{t\ ha^{-1}}\)
mafruit biomass of harvested organs \(\mathrm{t\ ha^{-1}}\)
mafruit_kg_ha Dry matter of harvested organs \(\mathrm{kg\ ha^{-1}}\)
maperenne biomass of perennial organs \(\mathrm{t\ ha^{-1}}\)
maperennemort biomass of dead perennial organs \(\mathrm{t\ ha^{-1}}\)
masec(n) biomass of aboveground plant (table) \(\mathrm{t\ ha^{-1}}\)
masec_kg_ha Aboveground dry matter \(\mathrm{kg\ ha^{-1}}\)
masec_mx_av_cut Aboveground dry matter before cut(for cut crops, for others = masec(n) ) \(\mathrm{t\ ha^{-1}}\)
masecneo biomass of newly-formed organs \(\mathrm{t\ ha^{-1}}\)
masecnp biomass of aerials and non perennial organs \(\mathrm{t\ ha^{-1}}\)
masectot total plant biomass (aerials + roots + perennial organs) \(\mathrm{t\ ha^{-1}}\)
masecveg biomass of vegetative organs \(\mathrm{t\ ha^{-1}}\)
matigestruc biomass of stems (only structural parts) \(\mathrm{t\ ha^{-1}}\)
matigestruc_kg_ha Dry matter of stems (only structural parts) \(\mathrm{kg\ ha^{-1}}\)
matuber biomass of tuber (harvested organs, only calculated for sugarbeet) \(\mathrm{t\ ha^{-1}}\)
mean_swfac_flo_p_m_150 swfac mean on the period flowering minus 150 degrees day to flowering plus 150 degrees days \(\mathrm{0\ to\ 1}\)
mortalle daily number of dying tillers \(\mathrm{day^{-1}}\)
mortmasec cumulative biomass of dead tillers \(\mathrm{t\ ha^{-1}}\)
mortreserve biomass of reserves corresponding to dead tillers \(\mathrm{t\ ha^{-1}\ day^{-1}}\)
MSexporte cumulative amount of harvested biomass \(\mathrm{t\ ha^{-1}}\)
msjaune senescent biomass of the plant \(\mathrm{t\ ha^{-1}}\)
msneojaune newly-formed senescent biomass \(\mathrm{t\ ha^{-1}}\)
msrac(n) biomass of roots \(\mathrm{t\ ha^{-1}}\)
msracf(1) biomass of fine roots in layer 1 \(\mathrm{t\ ha^{-1}}\)
msracf(2) biomass of fine roots in layer 2 \(\mathrm{t\ ha^{-1}}\)
msracf(3) biomass of fine roots in layer 3 \(\mathrm{t\ ha^{-1}}\)
msracf(4) biomass of fine roots in layer 4 \(\mathrm{t\ ha^{-1}}\)
msracf(5) biomass of fine roots in layer 5 \(\mathrm{t\ ha^{-1}}\)
msracg(1) biomass of coarse roots in layer 1 \(\mathrm{t\ ha^{-1}}\)
msracg(2) biomass of coarse roots in layer 2 \(\mathrm{t\ ha^{-1}}\)
msracg(3) biomass of coarse roots in layer 3 \(\mathrm{t\ ha^{-1}}\)
msracg(4) biomass of coarse roots in layer 4 \(\mathrm{t\ ha^{-1}}\)
msracg(5) biomass of coarse roots in layer 5 \(\mathrm{t\ ha^{-1}}\)
msracmort Biomass of dead roots \(\mathrm{t\ ha^{-1}}\)
msracmortf(1) cumulative biomass of dead fine roots in layer 1 \(\mathrm{t\ ha^{-1}}\)
msracmortf(2) cumulative biomass of dead fine roots in layer 2 \(\mathrm{t\ ha^{-1}}\)
msracmortf(3) cumulative biomass of dead fine roots in layer 3 \(\mathrm{t\ ha^{-1}}\)
msracmortf(4) cumulative biomass of dead fine roots in layer 4 \(\mathrm{t\ ha^{-1}}\)
msracmortf(5) cumulative biomass of dead fine roots in layer 5 \(\mathrm{t\ ha^{-1}}\)
msracmortg(1) cumulative biomass of dead coarse roots in layer 1 \(\mathrm{t\ ha^{-1}}\)
msracmortg(2) cumulative biomass of dead coarse roots in layer 2 \(\mathrm{t\ ha^{-1}}\)
msracmortg(3) cumulative biomass of dead coarse roots in layer 3 \(\mathrm{t\ ha^{-1}}\)
msracmortg(4) cumulative biomass of dead coarse roots in layer 4 \(\mathrm{t\ ha^{-1}}\)
msracmortg(5) cumulative biomass of dead coarse roots in layer 5 \(\mathrm{t\ ha^{-1}}\)
msrec_fou biomass of harvested forage \(\mathrm{t\ ha^{-1}}\)
msrec_fou_coupe Dry matter of harvested organs for forages at cutting \(\mathrm{t\ ha^{-1}}\)
msrec_fou_tot Dry matter of harvestable organs for forages cumulated over the USM \(\mathrm{t\ ha^{-1}}\)
MSrecycle cumulative amount of biomass returned to soil (unexported at harvest + fallen leaves) \(\mathrm{t\ ha^{-1}}\)
msresjaune senescent residual dry matter \(\mathrm{t\ ha^{-1}}\)
mstot biomass of whole plant (aerial + root + perennial organs) \(\mathrm{t\ ha^{-1}}\)
N_mineralisation cumulative amount of N mineralized from humus and organic residues \(\mathrm{kg\ ha^{-1}}\)
n_tot_irrigations total number of rrigations \(\mathrm{sd}\)
N_volatilisation cumulative amount of N volatilised from fertilizer and organic inputs \(\mathrm{kg\ ha^{-1}}\)
Nb amount of N in the microbial biomass decomposing organic residues mixed with soil \(\mathrm{kg\ ha^{-1}}\)
nb_days_frost_amf_120 number of days of tcultmin< tdebgel from amf stage to amf+120 degrees day \(\mathrm{days}\)
nb_days_humair_gt_90_percent1 number of days when humair_percent >=90% between amf and lax \(\mathrm{days}\)
nb_days_humair_gt_90_percent2 number of days when humair_percent >=90% between lax and drp \(\mathrm{days}\)
nbfeuille number of leaves on main stem \(\mathrm{ND}\)
nbinflo_recal number of inflorescences per plant \(\mathrm{ND}\)
nbj0remp number of shrivelling days \(\mathrm{days}\)
nbjechaudage number of shrivelling days between lax and rec \(\mathrm{days}\)
nbjgel number of frosting days active on the plant \(\mathrm{days}\)
nbjpourdecirecolte number of days until harvest is launched when it is postponed by the harvest decision option \(\mathrm{days}\)
nbjpourdecisemis number of days until sowing is launched when it is postponed by the sowing decision option \(\mathrm{days}\)
Nbmulch amount of N in microbial biomass decomposing the decomposable mulch \(\mathrm{kg\ ha^{-1}}\)
NCbio N/C ratio of biomass decomposing organic residues \(\mathrm{ND}\)
Ndenit daily denitrification rate in soil (if option denitrification is activated) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
Ndfa proportion of total plant N issued from N fixation \(\mathrm{0\ to\ 1}\)
Nexporte cumulative amount of N removed by crop harvests \(\mathrm{kg\ ha^{-1}}\)
nfruit(1) number of fruits in box 1 \(\mathrm{ND}\)
nfruit(2) number of fruits in box 2 \(\mathrm{ND}\)
nfruit(3) number of fruits in box 3 \(\mathrm{ND}\)
nfruit(4) number of fruits in box 4 \(\mathrm{ND}\)
nfruit(5) number of fruits in box 5 \(\mathrm{ND}\)
nfruit(nboite) number of fruits in last box \(\mathrm{ND}\)
nfruit(nboite-1) number of fruits in last but one box \(\mathrm{ND}\)
nfruitnou number of set fruits \(\mathrm{fruits\ m^{-2}}\)
Nhuma amount of N in active soil organic matter \(\mathrm{kg\ ha^{-1}}\)
Nhumi amount of N in inert soil organic matter \(\mathrm{kg\ ha^{-1}}\)
Nhumt amount of N in humus soil organic matter (active + inert fractions) \(\mathrm{kg\ ha^{-1}}\)
nit_1_30 amount of NO3-N in the soil layer 1 to 30 cm \(\mathrm{kg\ ha^{-1}}\)
nit_31_60 amount of NO3-N in the soil layer 31 to 60 cm \(\mathrm{kg\ ha^{-1}}\)
nit_61_90 amount of NO3-N in the soil layer 61 to 90 cm \(\mathrm{kg\ ha^{-1}}\)
soilN_rootdepth amount of NO3-N in soil in the maximum root depth \(\mathrm{kg\ ha^{-1}}\)
nitetcult(n) number of iterations to calculate tcult \(\mathrm{ND}\)
nitrifj daily nitrification rate in soil (if option nitrification is activated) \(\mathrm{kg\ ha^{-1}}\)
Nmineral_from_lev cumulative amount of N mineralized during the crop cycle ( emergence or budbreak-harvest) \(\mathrm{kg\ ha^{-1}}\)
Nmineral_from_plt cumulative amount of N mineralized during the crop cycle (sowing-harvest) \(\mathrm{kg\ ha^{-1}}\)
Nmulch amount of N in the plant mulch \(\mathrm{kg\ ha^{-1}}\)
Nmulchdec amount of N in the decomposable mulch \(\mathrm{kg\ ha^{-1}}\)
Nmulchnd amount of N in the non decomposable mulch \(\mathrm{kg\ ha^{-1}}\)
Nnondec(1) amount of N in the undecomposable mulch derived from residues type 1 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(10) amount of N in the undecomposable mulch derived from residues type 10 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(2) amount of N in the undecomposable mulch derived from residues type 2 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(3) amount of N in the undecomposable mulch derived from residues type 3 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(4) amount of N in the undecomposable mulch derived from residues type 4 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(5) amount of N in the undecomposable mulch derived from residues type 5 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(6) amount of N in the undecomposable mulch derived from residues type 6 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(7) amount of N in the undecomposable mulch derived from residues type 7 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(8) amount of N in the undecomposable mulch derived from residues type 8 \(\mathrm{kg\ ha^{-1}}\)
Nnondec(9) amount of N in the undecomposable mulch derived from residues type 9 \(\mathrm{kg\ ha^{-1}}\)
nodn reduction factor on nodulation establishment (potential BNF) due to mineral N stress \(\mathrm{0/^{1}}\)
Norgeng daily amount of N immobilized from fertiliser \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
Nr amount of N in the decomposing organic residues mixed with soil \(\mathrm{kg\ ha^{-1}}\)
Nrecycle cumulative amount of N returned to soil (unexported at harvest + fallen leaves) \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(1) amount of N in organic residues over the profhum depth, derived from residues type 1 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(10) amount of N in organic residues over the profhum depth, derived from residues type 10 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(2) amount of N in organic residues over the profhum depth, derived from residues type 2 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(3) amount of N in organic residues over the profhum depth, derived from residues type 3 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(4) amount of N in organic residues over the profhum depth, derived from residues type 4 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(5) amount of N in organic residues over the profhum depth, derived from residues type 5 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(6) amount of N in organic residues over the profhum depth, derived from residues type 6 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(7) amount of N in organic residues over the profhum depth, derived from residues type 7 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(8) amount of N in organic residues over the profhum depth, derived from residues type 8 \(\mathrm{kg\ ha^{-1}}\)
Nresiduprofil(9) amount of N in organic residues over the profhum depth, derived from residues type 9 \(\mathrm{kg\ ha^{-1}}\)
Nrprof amount of N in deep organic residues mixed with soil (below the profhum depth) \(\mathrm{kg\ ha^{-1}}\)
Nrtout total amount of N in organic residues present over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
Nsurplus Difference between N inputs and outputs to the soil, including organic fertilizer inputs \(\mathrm{kg\ ha^{-1}}\)
Nsurplus_min Difference between N inputs and outputs to the soil, without organic fertilizer inputs \(\mathrm{kg\ ha^{-1}}\)
numcoupe cut number \(\mathrm{ND}\)
numcult crop season number \(\mathrm{ND}\)
Nvolat_from_lev cumulative amount of N volatilised during the crop cycle( emergence or budbreak-harvest) \(\mathrm{kg\ ha^{-1}}\)
Nvolat_from_plt cumulative amount of N volatilised during the crop cycle (planting-harvest) \(\mathrm{kg\ ha^{-1}}\)
Nvoleng daily amount of N volatilised from fertiliser \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
Nvolorg daily amount of N volatilised from organic inputs \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
offrenod daily amount of N fixed symbiotically (BNF) \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
p1000grain 1000 grains weight (dry weight) \(\mathrm{g}\)
pdsfruit(1) weight of fruits in box 1 \(\mathrm{g\ m^{-2}}\)
pdsfruit(2) weight of fruits in box 2 \(\mathrm{g\ m^{-2}}\)
pdsfruit(3) weight of fruits in box 3 \(\mathrm{g\ m^{-2}}\)
pdsfruit(4) weight of fruits in box 4 \(\mathrm{g\ m^{-2}}\)
pdsfruit(5) weight of fruits in box 5 \(\mathrm{g\ m^{-2}}\)
pdsfruit(nboite) weight of fruits in last box \(\mathrm{g\ m^{-2}}\)
pdsfruit(nboite-1) weight of fruits in last but one box \(\mathrm{g\ m^{-2}}\)
pdsfruitfrais weight of fresh fruits \(\mathrm{g\ m^{-2}}\)
penfruit ratio of fruit envelops to plant biomass \(\mathrm{0\ to\ 1}\)
pfeuil(n) ratio of leaves to plant biomass \(\mathrm{0\ to\ 1}\)
pfeuiljaune ratio of yellow leaves to plant biomass \(\mathrm{0\ to\ 1}\)
pfeuilverte(n) ratio of green leaves to non-senescent plant biomass \(\mathrm{0\ to\ 1}\)
phoi photoperiod \(\mathrm{hour}\)
pHvol pH of soil surface as affected by organic residues application (slurry) \(\mathrm{ND}\)
pousfruit number of fruits transferred from one box to the next \(\mathrm{ND}\)
poussracmoy mean reduction factor on the root growth due to soil constraints (option true density) \(\mathrm{0\ to\ 1}\)
precip daily amount of water added to soil (precipitation + irrigation - mulch interception - runoff at the surface) \(\mathrm{mm\ day^{-1}}\)
precipjN daily amount of mineral N added to soil due to precipitation \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
precipN cumulative amount of mineral N added to soil due to precipitation \(\mathrm{kg\ ha^{-1}}\)
preciprec(n) recalculated daily precipitation \(\mathrm{mm\ day^{-1}}\)
preserve proportion of reserve in total plant biomass \(\mathrm{0\ to\ 1}\)
profexteau average depth of water absorption by plant \(\mathrm{cm}\)
profextN average depth of N absorption by plant \(\mathrm{cm}\)
profnappe depth of water table \(\mathrm{cm}\)
psibase predawn leaf water potential \(\mathrm{MPa}\)
ptigestruc proportion of structural stems in total plant biomass \(\mathrm{0\ to\ 1}\)
q_irrigations(1) amount of irrigation \(\mathrm{mm}\)
q_irrigations(10) amount of irrigation \(\mathrm{mm}\)
q_irrigations(11) amount of irrigation \(\mathrm{mm}\)
q_irrigations(12) amount of irrigation \(\mathrm{mm}\)
q_irrigations(13) amount of irrigation \(\mathrm{mm}\)
q_irrigations(14) amount of irrigation \(\mathrm{mm}\)
q_irrigations(15) amount of irrigation \(\mathrm{mm}\)
q_irrigations(16) amount of irrigation \(\mathrm{mm}\)
q_irrigations(17) amount of irrigation \(\mathrm{mm}\)
q_irrigations(18) amount of irrigation \(\mathrm{mm}\)
q_irrigations(19) amount of irrigation \(\mathrm{mm}\)
q_irrigations(2) amount of irrigation \(\mathrm{mm}\)
q_irrigations(20) amount of irrigation \(\mathrm{mm}\)
q_irrigations(21) amount of irrigation \(\mathrm{mm}\)
q_irrigations(22) amount of irrigation \(\mathrm{mm}\)
q_irrigations(23) amount of irrigation \(\mathrm{mm}\)
q_irrigations(24) amount of irrigation \(\mathrm{mm}\)
q_irrigations(25) amount of irrigation \(\mathrm{mm}\)
q_irrigations(26) amount of irrigation \(\mathrm{mm}\)
q_irrigations(27) amount of irrigation \(\mathrm{mm}\)
q_irrigations(28) amount of irrigation \(\mathrm{mm}\)
q_irrigations(29) amount of irrigation \(\mathrm{mm}\)
q_irrigations(3) amount of irrigation \(\mathrm{mm}\)
q_irrigations(30) amount of irrigation \(\mathrm{mm}\)
q_irrigations(4) amount of irrigation \(\mathrm{mm}\)
q_irrigations(5) amount of irrigation \(\mathrm{mm}\)
q_irrigations(6) amount of irrigation \(\mathrm{mm}\)
q_irrigations(7) amount of irrigation \(\mathrm{mm}\)
q_irrigations(8) amount of irrigation \(\mathrm{mm}\)
q_irrigations(9) amount of irrigation \(\mathrm{mm}\)
QCapp cumulative amount of organic C added to soil \(\mathrm{kg\ ha^{-1}}\)
QCO2hum cumulative amount of CO2-C emitted due to mineralisation of humus \(\mathrm{kg\ ha^{-1}}\)
QCO2mul cumulative amount of CO2-C emitted due to mineralisation of residues in the mulch \(\mathrm{kg\ ha^{-1}}\)
QCO2res cumulative amount of CO2-C emitted due to mineralisation of residues (including mulch) \(\mathrm{kg\ ha^{-1}}\)
QCO2sol cumulative amount of CO2-C emitted due to heterotrophic respiration (QCO2res + QCO2hum) \(\mathrm{kg\ ha^{-1}}\)
QCperennemort cumulative amount of C in dead perennial organs \(\mathrm{kg\ ha^{-1}}\)
QCperennemort2 cumulative amount of C in dead perennial organs of the two plants \(\mathrm{kg\ ha^{-1}}\)
QCplantetombe cumulative amount of C added to soil by fallen leaves due to senescence \(\mathrm{kg\ ha^{-1}}\)
QCplantetombe2 cumulative amount of C added to soil by fallen leaves due to senescence for the two plants \(\mathrm{kg\ ha^{-1}}\)
QCprimed cumulative amount of C mineralised by priming effect \(\mathrm{kg\ ha^{-1}}\)
QCrac amount of C in roots \(\mathrm{kg\ ha^{-1}}\)
QCrac amount of C in living roots \(\mathrm{kg\ ha^{-1}}\)
QCracmort cumulative amount of C added to soil by dead roots \(\mathrm{kg\ ha^{-1}}\)
QCracmort2 cumulative amount of C added to soil by dead roots of the two plants \(\mathrm{kg\ ha^{-1}}\)
QCresorg cumulative amount of C added to soil through organic exogenous residues \(\mathrm{kg\ ha^{-1}}\)
QCressuite cumulative amount of C added to soil due to aerial residues at harvest \(\mathrm{kg\ ha^{-1}}\)
QCressuite2 cumulative amount of C added to soil due to aerial residues at harvest for the two plants \(\mathrm{kg\ ha^{-1}}\)
QCressuite_tot cumulative amount of C added to soil by aerial residues from all harvests \(\mathrm{t\ ha^{-1}}\)
QCressuite_tot2 cumulative amount of C added to soil by aerial residues from all harvests of the two plants \(\mathrm{kg\ ha^{-1}}\)
QCrogne cumulative amount of C added to soil by fallen leaves due to trimming \(\mathrm{kg\ ha^{-1}}\)
QCrogne2 cumulative amount of C added to soil by fallen leaves due to trimming of the two plants \(\mathrm{kg\ ha^{-1}}\)
Qdrain water flow rate in mole drains \(\mathrm{mm\ day^{-1}}\)
Qdraincum cumulative amount of water flowing in mole drains \(\mathrm{mm}\)
Qem_N2O cumulative amount of N2O-N emitted from soil \(\mathrm{kg\ ha^{-1}}\)
Qem_N2Oden cumulative amount of N2O-N emitted from soil by denitrification \(\mathrm{kg\ ha^{-1}}\)
Qem_N2Onit cumulative amount of N2O-N emitted from soil by nitrification \(\mathrm{kg\ ha^{-1}}\)
qexport biomass exported out of the field \(\mathrm{t\ ha^{-1}}\)
Qfix amount of N fixed symbiotically (BNF) between two cuts \(\mathrm{kg\ ha^{-1}}\)
Qfixtot cumulative amount of N fixed symbiotically (BNF) \(\mathrm{kg\ ha^{-1}}\)
Qfixtot2 cumulative amount of N fixed symbiotically (BNF) by the two plants \(\mathrm{kg\ ha^{-1}}\)
Qles cumulative amount of NO3-N leached at the base of the soil profile \(\mathrm{kg\ ha^{-1}}\)
Qlesd cumulative amount of NO3-N leached into mole drains \(\mathrm{kg\ ha^{-1}}\)
Qmin cumulative amount of mineralized N from soil \(\mathrm{kg\ ha^{-1}}\)
Qminh cumulative amount of mineralized N derived from humus decomposition \(\mathrm{kg\ ha^{-1}}\)
Qminr cumulative amount of mineralized N derived from organic residues decomposition \(\mathrm{kg\ ha^{-1}}\)
qmulch biomass of plant mulch \(\mathrm{t\ ha^{-1}}\)
QNabso cumulative N absorbed by the crop (fixation not included) \(\mathrm{kg\ ha^{-1}}\)
QNabso2 cumulative N absorbed by the two crops (fixation not included) \(\mathrm{kg\ ha^{-1}}\)
QNabsoaer cumulative N absorbed by the crop and allocated to the aerials \(\mathrm{kg\ ha^{-1}}\)
QNabsoper cumulative N absorbed by the crop and allocated to the perennial organs \(\mathrm{kg\ ha^{-1}}\)
QNabsorac cumulative N absorbed by the crop and allocated to the roots \(\mathrm{kg\ ha^{-1}}\)
QNabsotot cumulative N taken up by the crop, including N fixation \(\mathrm{kg\ ha^{-1}}\)
QNapp cumulative amount of organic N added to soil (straw + roots + fallen leaves + organic fertilisers ) \(\mathrm{kg\ ha^{-1}}\)
QNdenit cumulative amount of N denitrified during the simulation period \(\mathrm{kg\ ha^{-1}}\)
QNdenit_from_lev cumulative amount of N denitrified during the crop cycle ( emergence or budbreak-harvest) \(\mathrm{kg\ ha^{-1}}\)
QNdenit_from_plt cumulative amount of N denitrified during the crop cycle \(\mathrm{kg\ ha^{-1}}\)
QNexport Amount of nitrogen exported at harvest (harvested and removed parts) \(\mathrm{kg\ ha^{-1}}\)
QNexport2 Amount of nitrogen exported at harvest from the two plants \(\mathrm{kg\ ha^{-1}}\)
QNfauche Amount of N exported in each cut \(\mathrm{kg\ ha^{-1}}\)
QNfauchetot Cumulative amount of N exported by all cuts \(\mathrm{kg\ ha^{-1}}\)
QNfauchetot2 Cumulative amount of N exported by all cuts of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNfeuille N content of structural part of the leaves \(\mathrm{kg\ ha^{-1}}\)
QNgaz cumulative amount of gaseous N losses (through volatilisation and denitrification) \(\mathrm{kg\ ha^{-1}}\)
QNgrain amount of N in harvested organs (grains / fruits) \(\mathrm{kg\ ha^{-1}}\)
Qnitrif cumulative amount of N nitrified in soil (if option nitrification is activated) \(\mathrm{kg\ ha^{-1}}\)
QNorgeng cumulative amount of N immobilized from fertiliser \(\mathrm{kg\ ha^{-1}}\)
QNperenne amount of N in perennial organs \(\mathrm{kg\ ha^{-1}}\)
QNperennemort cumulative amount of N in dead perennial organs \(\mathrm{kg\ ha^{-1}}\)
QNperennemort2 cumulative amount of N in dead perennial organs of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNplante amount of N in plants (aerial + perennial organs), without roots \(\mathrm{kg\ ha^{-1}}\)
QNplante_mx_av_cut Amount of nitrogen taken up by the plant before cut (for cut crops, for others = QNplante) \(\mathrm{kg\ ha^{-1}}\)
QNplantenp amount of N in non perennial organs (aerials + roots) \(\mathrm{kg\ ha^{-1}}\)
QNplantetombe cumulative amount of N added to soil by fallen leaves \(\mathrm{kg\ ha^{-1}}\)
QNplantetombe2 cumulative amount of N added to soil by fallen leaves of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNprimed cumulative amount of N mineralised by priming effect \(\mathrm{kg\ ha^{-1}}\)
QNrac amount of N in roots \(\mathrm{kg\ ha^{-1}}\)
QNracmort cumulative amount of N added to soil by dead roots \(\mathrm{kg\ ha^{-1}}\)
QNracmort2 cumulative amount of N added to soil by dead roots of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNresorg cumulative amount of organic exogenous N added to soil \(\mathrm{kg\ ha^{-1}}\)
QNresperenne amount of N in perennial reserves \(\mathrm{kg\ ha^{-1}}\)
QNresperennestruc amount of N in the structural pool of perennial organs \(\mathrm{kg\ ha^{-1}}\)
QNressuite cumulative amount of N added to soil by aerial residues at harvest \(\mathrm{kg\ ha^{-1}}\)
QNressuite_tot cumulative amount of N added to soil by aerial residues from all harvests \(\mathrm{kg\ ha^{-1}}\)
QNressuite_tot2 cumulative amount of N added to soil by aerial residues from all harvests of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNressuite2 cumulative amount of N added to soil by aerial residues of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNrestemp amount of N in temporary reserves of vegetative organs that can be remobilised \(\mathrm{kg\ ha^{-1}}\)
QNrogne cumulative amount of N added to soil due to trimming \(\mathrm{kg\ ha^{-1}}\)
QNrogne2 cumulative amount of N added to soil due to trimming of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNtige Structural nitrogen content in stems \(\mathrm{kg\ ha^{-1}}\)
QNtot amount of N in whole plant (aerial + root + perennial organs) \(\mathrm{kg\ ha^{-1}}\)
QNtot2 amount of N in whole plant (aerial + root + perennial organs) of the two plants \(\mathrm{kg\ ha^{-1}}\)
QNveg amount of N in vegetative organs \(\mathrm{kg\ ha^{-1}}\)
QNvegstruc amount of N in the structural part of vegetative organs \(\mathrm{kg\ ha^{-1}}\)
QNvoleng cumulative amount of N volatilised from fertiliser \(\mathrm{kg\ ha^{-1}}\)
QNvolorg cumulative amount of N volatilised from organic inputs \(\mathrm{kg\ ha^{-1}}\)
qres_pature amount of crop residue by pasture applied to the soil (fresh weight) \(\mathrm{t\ MF\ ha^{-1}}\)
Qressuite biomass of residues from the previous crop returned to soil at harvest (without fallen leaves) \(\mathrm{t\ ha^{-1}}\)
Qressuite_tot amount of total harvest residues (aerials + roots) \(\mathrm{t\ ha^{-1}}\)
ra_recal aerodynamic resistance between the canopy and the reference level zr \(\mathrm{s\ m^{-1}}\)
raint photosynthetic active radiation intercepted by the canopy \(\mathrm{MJ\ m^{-2}}\)
ras aerodynamic resistance between the soil and the canopy \(\mathrm{s\ m^{-1}}\)
ratioFT Leaves to stem ratio \(\mathrm{ND}\)
Ratm atmospheric radiation \(\mathrm{MJ\ m^{-2}}\)
rc resistance of canopy \(\mathrm{s\ m^{-1}}\)
rdif ratio of diffuse radiation to global radiation \(\mathrm{0\ to\ 1}\)
remobilj daily amount of biomass remobilized for growth \(\mathrm{kg\ ha^{-1}\ day^{-1}}\)
remontee capillary uptake from the base of the soil profile \(\mathrm{mm\ day^{-1}}\)
rendementsec biomass of harvested organs (0% moisture) \(\mathrm{t\ ha^{-1}}\)
resmes amount of soil water integrated on the measurement depth \(\mathrm{mm}\)
resperenne biomass of metabolic reserves in the perennial organs \(\mathrm{t\ ha^{-1}}\)
resrac soil water reserve in the root zone \(\mathrm{mm}\)
restemp biomass reserves (carbohydrates) in shoots that can be accumulated or mobilized for crop growth \(\mathrm{t\ ha^{-1}}\)
rfpi reduction factor on plant development due to photoperiod \(\mathrm{0\ to\ 1}\)
rfvi reduction factor on plant development due to vernalization \(\mathrm{0\ to\ 1}\)
rlj rate of root length growth \(\mathrm{m\ day^{-1}}\)
rltot total root length (accounting for senescent roots) \(\mathrm{cm\ cm^{-2}}\)
rltotf total root length (accounting for senescent roots) \(\mathrm{cm\ cm^{-2}}\)
rltotg total root length (accounting for senescent roots) \(\mathrm{cm\ cm^{-2}}\)
rmaxi maximum water reserve used \(\mathrm{mm}\)
rnet net radiation \(\mathrm{MJ\ m^{-2}}\)
rnetS net radiation at the soil surface \(\mathrm{MJ\ m^{-2}}\)
rombre fraction of the total radiation in the shade \(\mathrm{0\ to\ 1}\)
rsoleil fraction of the total radiation in the full sun \(\mathrm{0\ to\ 1}\)
RsurRU fraction of plant available water over the soil profile \(\mathrm{0\ to\ 1}\)
RsurRUrac fraction of plant available water over the root profile \(\mathrm{0\ to\ 1}\)
RU plant available water content over the soil profile \(\mathrm{mm}\)
ruissel daily amount of water in total runoff (surface + overflow) \(\mathrm{mm\ day^{-1}}\)
ruisselsurf daily amount of water in runoff at soil surface \(\mathrm{mm\ day^{-1}}\)
ruisselt cumulative amount of water in total runoff (surface + overflow) \(\mathrm{mm}\)
runoff_from_lev cumulative amount of water in runoff (surface + overflow) during the crop cycle ( emergence or budbreak-harvest) \(\mathrm{mm}\)
runoff_from_plt cumulative amount of water in runoff (surface + overflow) during the crop cycle (sowing-harvest) \(\mathrm{mm}\)
RUrac maximum plant available water content over the root profile \(\mathrm{mm}\)
saturation amount of water in the soil macroporosity \(\mathrm{mm}\)
Sdepth(n) snow cover depth \(\mathrm{m}\)
senfac reduction factor on leaf life span due to water stress (increasing senescence rate) \(\mathrm{0\ to\ 1}\)
sla specific leaf area \(\mathrm{cm^{2}\ g^{-1}}\)
SMN amount of soil mineral N content over the soil profile \(\mathrm{kg\ ha^{-1}}\)
SMNmes amount of soil mineral N content over the depth profmes \(\mathrm{kg\ ha^{-1}}\)
Snowaccu(n) daily snowfall accumulation (mm water equivalent) \(\mathrm{mm\ day^{-1}}\)
Snowmelt(n) daily snowmelt (mm water equivalent) \(\mathrm{mm\ day^{-1}}\)
SOC amount of soil organic C (= Chumt + Cb) over the profhum depth \(\mathrm{kg\ ha^{-1}}\)
SOCL(1) amount of soil organic C (= Chumt + Cb) in the layer 1 \(\mathrm{kg\ ha^{-1}}\)
SOCL(2) amount of soil organic C (= Chumt + Cb) in the layer 2 \(\mathrm{kg\ ha^{-1}}\)
SOCL(3) amount of soil organic C (= Chumt + Cb) in the layer 3 \(\mathrm{kg\ ha^{-1}}\)
SOCL(4) amount of soil organic C (= Chumt + Cb) in the layer 4 \(\mathrm{kg\ ha^{-1}}\)
SOCL(5) amount of soil organic C (= Chumt + Cb) in the layer 5 \(\mathrm{kg\ ha^{-1}}\)
SOC0 amount of soil organic C (= Chumt + Cb) over the profhum depth at time 0 \(\mathrm{kg\ ha^{-1}}\)
SOCbalance Soil organic C balance (inputs-outputs) over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
SOCinputs Soil organic C inputs to the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
SOCtot amount of soil organic C (all organic pools) over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
SoilAvW amount of plant available water in soil over the depth profmes \(\mathrm{mm}\)
SoilAvW_by_layers(1) \(\mathrm{}\)
SoilAvW_by_layers(2) \(\mathrm{}\)
SoilAvW_by_layers(3) \(\mathrm{}\)
SoilAvW_by_layers(4) \(\mathrm{}\)
SoilAvW_by_layers(5) \(\mathrm{}\)
SoilN amount of mineral N in soil over the depth profmes \(\mathrm{kg\ ha^{-1}}\)
SoilNM amount of NO3-N in soil over the depth profmesN \(\mathrm{kg\ ha^{-1}}\)
SoilWatM amount of plant available water in soil over the depth profmesW \(\mathrm{mm}\)
som_HUR cumulative water content of the soil microporosity \(\mathrm{mm}\)
som_sat cumulative amount of water in the soil macroporosity \(\mathrm{mm}\)
somcour cumulative units of development (upvt) between two stages \(\mathrm{^{\circ}C\ d}\)
somcourdrp cumulative units of development (upvt) between two reproductive stages \(\mathrm{^{\circ}C\ d}\)
somcourfauche sum of temperature beetwen 2 cuts of forage crop \(\mathrm{^{\circ}C\ d}\)
somcourmont cumulative units of development from the start of vernalisation \(\mathrm{^{\circ}C\ d}\)
somdifftculttair cumulative temperature difference (tcult-tair) during the simulation period \(\mathrm{^{\circ}C}\)
somtemp sum of temperatures (expressed in Q10 =sum (2.0 ** (udevair ou udevcult / 10.)) \(\mathrm{^{\circ}C\ d}\)
somudevair sum of air temperature (udevair) from sowing to harvest \(\mathrm{^{\circ}C}\)
somudevcult sum of crop temperature (udevcult) from sowing to harvest \(\mathrm{^{\circ}C}\)
somupvtsem sum of development units (upvt) from sowing to harvest \(\mathrm{^{\circ}C}\)
SON amount of soil organic N (= Nhumt + Nb) over the profhum depth \(\mathrm{kg\ ha^{-1}}\)
SONL(1) amount of soil organic N (= Nhumt + Nb) in the layer 1 \(\mathrm{kg\ ha^{-1}}\)
SONL(2) amount of soil organic N (= Nhumt + Nb) in the layer 2 \(\mathrm{kg\ ha^{-1}}\)
SONL(3) amount of soil organic N (= Nhumt + Nb) in the layer 3 \(\mathrm{kg\ ha^{-1}}\)
SONL(4) amount of soil organic N (= Nhumt + Nb) in the layer 4 \(\mathrm{kg\ ha^{-1}}\)
SONL(5) amount of soil organic N (= Nhumt + Nb) in the layer 5 \(\mathrm{kg\ ha^{-1}}\)
SON0 amount of soil organic N (= Nhumt + Nb) over the profhum depth at time 0 \(\mathrm{kg\ ha^{-1}}\)
SONbalance Soil organic N balance (inputs-outputs) over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
SONinputs Soil organic N inputs to the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
SONtot amount of soil organic N (all organic pools) over the whole soil profile \(\mathrm{kg\ ha^{-1}}\)
sourcepuits source to sink ratio of assimilates in the plant \(\mathrm{ND}\)
spfruit reduction factor on the fruits number due to trophic stress \(\mathrm{0\ to\ 1}\)
splai source to sink ratio of assimilates in the leaves \(\mathrm{ND}\)
stemflow daily amount of water runoff along the stem \(\mathrm{mm\ day^{-1}}\)
STN total soil N (mineral + organic) \(\mathrm{kg\ ha^{-1}}\)
str1intercoupe average stomatal water stress index during the vegetative phase (emergence - maximum LAI) of forage crops \(\mathrm{0\ to\ 1}\)
str2intercoupe average stomatal water stress index during the reproductive phase (maximum LAI - maturity) of forage crops \(\mathrm{0\ to\ 1}\)
stu1intercoupe average turgescence water stress index during the vegetative phase (emergence - maximum LAI) of forage crops \(\mathrm{0\ to\ 1}\)
stu2intercoupe average turgescence water stress index during the reproductive phase (maximum LAI - maturity) of forage crops \(\mathrm{0\ to\ 1}\)
sucre sugar content of harvested organs \(\mathrm{0\ to\ 1}\)
sucre_percent sugar content of harvested organs \(\mathrm{\%\ fresh\ weight}\)
surf(ao) fraction of the soil surface in the shade \(\mathrm{0\ to\ 1}\)
surf(as) fraction of the soil surface in the sun \(\mathrm{0\ to\ 1}\)
swfac stomatic water stress index \(\mathrm{0\ to\ 1}\)
swfac1moy average stomatic water stress index over the vegetative stage \(\mathrm{0\ to\ 1}\)
swfac2moy average stomatic water stress index over the reproductive stage \(\mathrm{0\ to\ 1}\)
tairveille mean air temperature at the previous day \(\mathrm{^{\circ}C}\)
tauxcouv(n) cover rate of the canopy \(\mathrm{ND}\)
tcult crop surface temperature (daily average) \(\mathrm{^{\circ}C}\)
tcult_tairveille difference between canopy temperature and air temperature \(\mathrm{^{\circ}C}\)
tcultmax crop surface temperature (daily maximum) \(\mathrm{^{\circ}C}\)
tcultmin crop surface temperature (daily minimum) \(\mathrm{^{\circ}C}\)
tempeff efficient temperature for growth \(\mathrm{^{\circ}C}\)
tetp(n) efficient potential evapotranspiration (entered or calculated) \(\mathrm{mm\ day^{-1}}\)
tetstomate threshold of soil water content limiting transpiration and photosynthesis \(\mathrm{\%\ vol}\)
teturg threshold of soil water content limiting the growth of leaves (in surface area) \(\mathrm{\%\ vol}\)
tmax(n) maximum active temperature of atmosphere \(\mathrm{^{\circ}C}\)
tmaxext(n) maximum temperature of external atmosphere \(\mathrm{^{\circ}C}\)
tmaxrec(n) recalculated daily maximum temperature (with presence of a snow cover) \(\mathrm{^{\circ}C}\)
tmin(n) minimum active temperature of atmosphere \(\mathrm{^{\circ}C}\)
tminext(n) minimum temperature of external atmsphere \(\mathrm{^{\circ}C}\)
tminrec(n) recalculated daily minimum temperature (with presence of a snow cover) \(\mathrm{^{\circ}C}\)
tmoy(n) mean active temperature of atmosphere \(\mathrm{^{\circ}C}\)
tmoyext(n) mean temperature of external atmosphere \(\mathrm{^{\circ}C}\)
tmoyIpltJuin mean temperature from sowing or planting (iplt stage) until June 30 \(\mathrm{^{\circ}C}\)
tmoyIpltSept mean temperature from sowing or planting (iplt stage) until September 30 \(\mathrm{^{\circ}C}\)
tncultmat average of minimum crop temperatures (tcultmin) between the stages lax and rec \(\mathrm{^{\circ}C}\)
tnhc cumulative normalized time for the mineralisation of humus \(\mathrm{days}\)
tnrc cumulative normalized time for the mineralisation of organic residues \(\mathrm{days}\)
totapN cumulative amount of mineral N added by mineral fertilisers and organic fertilisers \(\mathrm{kg\ ha^{-1}}\)
totapNres cumulative amount of mineral N added by organic fertilisers \(\mathrm{kg\ ha^{-1}}\)
totir cumulative amount of water inputs (precipitation + irrigation) \(\mathrm{mm}\)
tpm(n) water vapour pressure in air \(\mathrm{hPa}\)
trg(n) active radiation (entered or calculated) \(\mathrm{MJ\ m^{-2}}\)
trgext(n) exterior radiation \(\mathrm{MJ\ m^{-2}}\)
trr(n) daily rainfall \(\mathrm{mm\ day^{-1}}\)
TS(1) mean soil temperature (in layer 1) \(\mathrm{^{\circ}C}\)
TS(2) mean soil temperature (in layer 2) \(\mathrm{^{\circ}C}\)
TS(3) mean soil temperature (in layer 3) \(\mathrm{^{\circ}C}\)
TS(4) mean soil temperature (in layer 4) \(\mathrm{^{\circ}C}\)
TS(5) mean soil temperature (in layer 5) \(\mathrm{^{\circ}C}\)
tsol(10) temperature in the soil at 10 cm \(\mathrm{degrees}\)
tsol_mean_0_profsem daily min soil temperature on the layer 1 to sowing depth \(\mathrm{days}\)
tsol_mean_ger_lev_0_dpthsow mean soil temperature on the layer 1 to sowing depth from germination date to emergence \(\mathrm{^{\circ}C\ d}\)
tsol_mean_plt_ger_0_dpthsow mean soil temperature on the layer 1 to sowing depth from sowing date to germination \(\mathrm{^{\circ}C\ d}\)
tsol_min_0_profsem daily mean soil temperature on the layer 1 to sowing depth \(\mathrm{days}\)
tsol_min_ger_lev_0_dpthsow min soil temperature on the layer 1 to sowing depth from germination date to emergence \(\mathrm{^{\circ}C\ d}\)
tsol_min_plt_ger_0_dpthsow min soil temperature on the layer 1 to sowing depth from sowing date to germination \(\mathrm{^{\circ}C\ d}\)
turfac turgescence water stress index \(\mathrm{0\ to\ 1}\)
turfac1moy average turgescence water stress index during the vegetative stage \(\mathrm{0\ to\ 1}\)
turfac2moy average turgescence water stress index during the reproductive stage \(\mathrm{0\ to\ 1}\)
tustress reduction factor on leaf growth due to the effective water stress (= min(turfac,innlai)) \(\mathrm{0\ to\ 1}\)
tvent(n) mean daily wind speed at 2 m high above soil \(\mathrm{m\ s^{-1}}\)
udevair effective temperature for crop development, computed with tair \(\mathrm{^{\circ}C\ d}\)
udevcult effective temperature for crop development, computed with tcult \(\mathrm{^{\circ}C\ d}\)
ulai(n) relative development unit for LAI \(\mathrm{0\ to\ 3}\)
upvt(n) development unit \(\mathrm{^{\circ}C\ d}\)
urac daily relative development unit for root growth \(\mathrm{0^{1}-mars}\)
vitmoy mean canopy growth rate \(\mathrm{g\ m^{-2}\ day^{-1}}\)
xmlch1 thickness of the dry layer created by evaporation from the soil and mulch \(\mathrm{cm}\)
zrac maximum depth reached by root system \(\mathrm{cm}\)
zracmax maximum rooting depth \(\mathrm{cm}\)

  1. APP : Agence pour la protection des programmes↩︎